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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
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-rw-r--r--sci-biology/profphd/metadata.xml5
-rw-r--r--sci-biology/profphd/profphd-1.0.39.ebuild38
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-rw-r--r--sci-biology/psipred/files/2.6.1-Makefile.patch42
-rw-r--r--sci-biology/psipred/files/2.6.1-path.patch34
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-rw-r--r--sci-biology/psipred/metadata.xml8
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-rw-r--r--sci-biology/psipred/psipred-3.2.1.ebuild52
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-rw-r--r--sci-biology/qrna/Manifest1
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-rw-r--r--sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch328
-rw-r--r--sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch28
-rw-r--r--sci-biology/qrna/metadata.xml5
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-rw-r--r--sci-biology/raxml/Manifest1
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-rw-r--r--sci-biology/readseq/metadata.xml9
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-rw-r--r--sci-biology/rmblast/metadata.xml5
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-rw-r--r--sci-biology/rnaview/files/rnaview-20040713-implicit.patch13
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-rw-r--r--sci-biology/rnaview/metadata.xml13
-rw-r--r--sci-biology/rnaview/rnaview-20040713-r2.ebuild34
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-rw-r--r--sci-biology/samtools/Manifest5
-rw-r--r--sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch183
-rw-r--r--sci-biology/samtools/files/samtools-1.0-buildsystem.patch59
-rw-r--r--sci-biology/samtools/files/samtools-1.1-buildsystem.patch153
-rw-r--r--sci-biology/samtools/files/samtools-1.2-buildsystem.patch193
-rw-r--r--sci-biology/samtools/metadata.xml8
-rw-r--r--sci-biology/samtools/samtools-0.1.12.ebuild31
-rw-r--r--sci-biology/samtools/samtools-0.1.19-r2.ebuild61
-rw-r--r--sci-biology/samtools/samtools-1.0-r1.ebuild73
-rw-r--r--sci-biology/samtools/samtools-1.0.ebuild69
-rw-r--r--sci-biology/samtools/samtools-1.1.ebuild83
-rw-r--r--sci-biology/samtools/samtools-1.2.ebuild83
-rw-r--r--sci-biology/seaview/Manifest1
-rw-r--r--sci-biology/seaview/metadata.xml12
-rw-r--r--sci-biology/seaview/seaview-4.3.5.ebuild77
-rw-r--r--sci-biology/seqan/Manifest3
-rw-r--r--sci-biology/seqan/files/seqan-1.4.2-include.patch16
-rw-r--r--sci-biology/seqan/files/seqan-1.4.2-shared.patch22
-rw-r--r--sci-biology/seqan/files/seqan-2.0.0-zlib.patch15
-rw-r--r--sci-biology/seqan/metadata.xml5
-rw-r--r--sci-biology/seqan/seqan-1.3.1-r1.ebuild42
-rw-r--r--sci-biology/seqan/seqan-1.4.2.ebuild69
-rw-r--r--sci-biology/seqan/seqan-2.0.0.ebuild51
-rw-r--r--sci-biology/shrimp/Manifest2
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-rw-r--r--sci-biology/shrimp/shrimp-2.2.3.ebuild83
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-rw-r--r--sci-biology/sibsim4/sibsim4-0.20.ebuild36
-rw-r--r--sci-biology/sim4/Manifest1
-rw-r--r--sci-biology/sim4/metadata.xml21
-rw-r--r--sci-biology/sim4/sim4-20030921-r1.ebuild26
-rw-r--r--sci-biology/sim4/sim4-20030921.ebuild19
-rw-r--r--sci-biology/snpfile/Manifest1
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-rw-r--r--sci-biology/snpfile/snpfile-2.0.1.ebuild26
-rw-r--r--sci-biology/stride/Manifest2
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-rw-r--r--sci-biology/stride/metadata.xml5
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-rw-r--r--sci-biology/tophat/metadata.xml8
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-rw-r--r--sci-biology/tophat/tophat-1.4.1.ebuild32
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-rw-r--r--sci-biology/transfac/Manifest1
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-rw-r--r--sci-biology/transfac/transfac-3.2.ebuild41
-rw-r--r--sci-biology/tree-puzzle/Manifest1
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-rw-r--r--sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild57
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-rw-r--r--sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch77
-rw-r--r--sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch14
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-rw-r--r--sci-biology/treeviewx/files/treeviewx-wxt.patch50
-rw-r--r--sci-biology/treeviewx/metadata.xml11
-rw-r--r--sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild32
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-rw-r--r--sci-biology/trnascan-se/Manifest2
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-rw-r--r--sci-biology/trnascan-se/metadata.xml12
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-rw-r--r--sci-biology/ucsc-genome-browser/Manifest1
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-rw-r--r--sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch39
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-rw-r--r--sci-biology/velvet/Manifest2
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-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch10
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-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch18
-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch26
-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py27
-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch10
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-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch30
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-rw-r--r--sci-biology/yass/yass-1.14.ebuild22
801 files changed, 30735 insertions, 0 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild
new file mode 100644
index 000000000000..c76b28f8893a
--- /dev/null
+++ b/sci-biology/ApE/ApE-2.0.7-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="A Plasmid Editor"
+HOMEPAGE="http://www.biology.utah.edu/jorgensen/wayned/ape/"
+SRC_URI="http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip"
+
+LICENSE="ApE"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="app-arch/unzip"
+RDEPEND="
+ dev-lang/tcl:0
+ dev-lang/tk:0"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/ApE Linux/"
+
+src_compile() { :; }
+
+src_install() {
+ cat >> "${T}/ApE" <<- "EOF"
+ #!/bin/bash
+ cmdArgs=""
+
+ # AppMain.tcl searches files relative to the directory where it resides.
+ # Add absolute path to file here, if necessary.
+ for rfpath in "$@"; do
+ afpath="$PWD/${rfpath}"
+ if test -r "${afpath}"; then
+ cmdArgs="${cmdArgs} \"${afpath}\"";
+ else
+ cmdArgs="${cmdArgs} \"${rfpath}\"";
+ fi
+ done
+
+ eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}"
+ EOF
+
+ dobin "${T}/ApE"
+ insinto "/usr/share/${P}"
+ doins -r "${WORKDIR}"/ApE\ Linux/*
+ make_desktop_entry ${PN} ${PN} \
+ "/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \
+ "Science"
+}
diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest
new file mode 100644
index 000000000000..c8bc584062a7
--- /dev/null
+++ b/sci-biology/ApE/Manifest
@@ -0,0 +1 @@
+DIST ApE-2.0.7.zip 318454 SHA256 9d718562ef250b68dfad1de7d4179540fc04c001b0fdc5e9bd70f3605561bc32 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254 WHIRLPOOL d13e8a997c36f8e7ac951a17c195a714a243292f9a99f524758b09b1fdc9f436b11cf1124ac1a3527ff70aa8cc6dc9ac516a910246f9f6e4f8376c78e8b44013
diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml
new file mode 100644
index 000000000000..4252fbfae02e
--- /dev/null
+++ b/sci-biology/ApE/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>je_fro@gentoo.org</email>
+ <name>Jeff Gardner</name>
+ </maintainer>
+ <longdescription lang="en">
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
new file mode 100644
index 000000000000..a3c0228b819d
--- /dev/null
+++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MODULE_AUTHOR=LDS
+inherit perl-module webapp
+
+DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser"
+HOMEPAGE="http://gmod.org/wiki/GBrowse"
+KEYWORDS="~amd64 ~x86"
+IUSE="-minimal mysql postgres +sqlite"
+
+SLOT="0"
+WEBAPP_MANUAL_SLOT="yes"
+
+CDEPEND="!<sci-biology/GBrowse-2.44-r1
+ >=sci-biology/bioperl-1.6.9
+ >=dev-perl/Bio-Graphics-2.09
+ >=dev-perl/GD-2.07
+ >=dev-perl/CGI-Session-4.02
+ dev-perl/IO-String
+ dev-perl/JSON
+ dev-perl/libwww-perl
+ dev-perl/Statistics-Descriptive
+ !minimal? (
+ dev-perl/Bio-Das
+ >=dev-perl/Bio-SamTools-1.20
+ dev-perl/Crypt-SSLeay
+ dev-perl/DB_File-Lock
+ dev-perl/DBI
+ mysql? ( dev-perl/DBD-mysql )
+ postgres? ( dev-perl/DBD-Pg )
+ sqlite? ( dev-perl/DBD-SQLite )
+ dev-perl/FCGI
+ dev-perl/File-NFSLock
+ dev-perl/GD-SVG
+ dev-perl/Net-OpenID-Consumer
+ dev-perl/Net-SMTP-SSL
+ )"
+# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile
+DEPEND="dev-perl/Module-Build
+ dev-perl/Capture-Tiny
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch )
+
+src_configure() {
+ webapp_src_preinst
+
+# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse"
+ myconf="--conf=/etc/gbrowse2"
+ myconf="${myconf} --htdocs=${MY_HTDOCSDIR}"
+ myconf="${myconf} --cgibin=${MY_CGIBINDIR}"
+ myconf="${myconf} --tmp=/var/tmp/gbrowse2"
+ myconf="${myconf} --persistent=/var/db/gbrowse2"
+ myconf="${myconf} --databases=/var/db/gbrowse2/databases"
+ myconf="${myconf} --installconf=no"
+ myconf="${myconf} --installetc=no"
+ perl-module_src_configure
+}
+
+src_install() {
+ dodir /var/tmp/gbrowse2
+ dodir /var/db/gbrowse2/sessions
+ dodir /var/db/gbrowse2/userdata
+ webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2
+ perl-module_src_install
+ webapp_src_install
+}
diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest
new file mode 100644
index 000000000000..204fe59d5aa7
--- /dev/null
+++ b/sci-biology/GBrowse/Manifest
@@ -0,0 +1 @@
+DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135
diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
new file mode 100644
index 000000000000..5aa0be9df918
--- /dev/null
+++ b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
@@ -0,0 +1,72 @@
+diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm
+--- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000
++++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000
+@@ -454,33 +454,33 @@
+ $gid =~ /^(\d+)$/;
+ $gid = $1;
+
+- unless (chown $uid,$gid,$tmp) {
+- $self->ownership_warning($tmp,$user);
+- }
++# unless (chown $uid,$gid,$tmp) {
++# $self->ownership_warning($tmp,$user);
++# }
+
+ my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
+ my $images = File::Spec->catfile($tmp,'images');
+ my $htdocs = $self->install_path->{htdocs};
+- chown $uid,-1,$htdocs;
++# chown $uid,-1,$htdocs;
+ {
+ local $> = $uid;
+- symlink($images,$htdocs_i); # so symlinkifowner match works!
++# symlink($images,$htdocs_i); # so symlinkifowner match works!
+ }
+- chown $>,-1,$self->install_path->{htdocs};
++# chown $>,-1,$self->install_path->{htdocs};
+
+ my $persistent = $self->install_path->{'persistent'};
+ my $sessions = File::Spec->catfile($persistent,'sessions');
+ my $userdata = File::Spec->catfile($persistent,'userdata');
+- mkpath([$sessions,$userdata],0711);
++# mkpath([$sessions,$userdata],0711);
+
+ my $databases = $self->install_path->{'databases'};
+
+- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
+- $self->ownership_warning($databases,$user);
+- }
++# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
++# $self->ownership_warning($databases,$user);
++# }
+
+- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+- $self->fix_selinux;
++ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
++ # $self->fix_selinux;
+
+ my $base = basename($self->install_path->{htdocs});
+
+@@ -489,14 +489,14 @@
+ my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
+ my $perl = $self->perl;
+ my @inc = map{"-I$_"} split ':',$self->added_to_INC;
+- system $perl,@inc,$metadb_script;
+- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
++# system $perl,@inc,$metadb_script;
++# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
+
+- if (Module::Build->y_n(
+- "It is recommended that you restart Apache. Shall I try this for you?",'y'
+- )) {
+- system "sudo /etc/init.d/apache2 restart";
+- }
++# if (Module::Build->y_n(
++# "It is recommended that you restart Apache. Shall I try this for you?",'y'
++# )) {
++# system "sudo /etc/init.d/apache2 restart";
++# }
+
+ print STDERR "\n***INSTALLATION COMPLETE***\n";
+ print STDERR "Load http://localhost/$base for demo and documentation.\n";
+Only in GBrowse-2.39/install_util: GBrowseInstall.pm~
diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml
new file mode 100644
index 000000000000..32b15c723f9d
--- /dev/null
+++ b/sci-biology/GBrowse/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<upstream>
+ <remote-id type="cpan">GBrowse</remote-id>
+</upstream>
+</pkgmetadata>
diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest
new file mode 100644
index 000000000000..7b3eeafe5263
--- /dev/null
+++ b/sci-biology/aaindex/Manifest
@@ -0,0 +1 @@
+DIST aaindex-9.1.tar.bz2 133780 RMD160 6f5bd699de3c84bd366f9747f57712ba8aecf513 SHA1 7215e3dae85cd61919854ba5dd5abff29be91852 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa
diff --git a/sci-biology/aaindex/aaindex-9.1.ebuild b/sci-biology/aaindex/aaindex-9.1.ebuild
new file mode 100644
index 000000000000..6c45282be145
--- /dev/null
+++ b/sci-biology/aaindex/aaindex-9.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Amino acid indices and similarity matrices"
+LICENSE="public-domain"
+HOMEPAGE="http://www.genome.ad.jp/aaindex"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir AAINDEX
+ echo
+ einfo "Indexing AAindex for usage with EMBOSS."
+ EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die \
+ "Indexing AAindex failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins ${PN}{1,2,3} || die "Failed to install raw database."
+ fi
+ dodoc ${PN}.doc || die "Failed to install documentation."
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/AAINDEX
+ doins AAINDEX/* || die "Failed to install EMBOSS data files."
+ fi
+}
diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml
new file mode 100644
index 000000000000..ccb567e64e02
--- /dev/null
+++ b/sci-biology/aaindex/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ Amino acid indices and similarity matrices maintained at Kyoto
+ University. An amino acid index is a set of 20 numerical values
+ representing any of the different physicochemical and biological
+ properties of amino acids. The AAindex1 section of the Amino Acid
+ Index Database is a collection of published indices together with the
+ result of cluster analysis using the correlation coefficient as the
+ distance between two indices. This section currently contains 494
+ indices. Another important feature of amino acids that can be
+ represented numerically is the similarity between amino acids. Thus, a
+ similarity matrix, also called a mutation matrix, is a set of 210
+ numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
+ for sequence alignments and similarity searches. The AAindex2 section
+ of the Amino Acid Index Database is a collection of published amino
+ acid mutation matrices together with the result of cluster analysis.
+ This section currently contains 83 matrices.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
new file mode 100644
index 000000000000..77dfde1ec9c8
--- /dev/null
+++ b/sci-biology/abyss/Manifest
@@ -0,0 +1,3 @@
+DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
+DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01
+DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild
new file mode 100644
index 000000000000..08a82e2f692a
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit autotools eutils toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="amd64 x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+src_prepare() {
+ tc-export AR
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch \
+ "${FILESDIR}"/${P}-ac_prog_ar.patch
+
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \
+ $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild
new file mode 100644
index 000000000000..e230da8847ff
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.4.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
+ )
+
+src_prepare() {
+ tc-export AR
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --docdir="${EPREFIX}/usr/share/doc/${PF}"
+ $(use_enable openmp)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild
new file mode 100644
index 000000000000..04dcc7ce6a25
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.6.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ "${FILESDIR}"/${P}-ac_prog_ar.patch
+ )
+
+src_prepare() {
+ tc-export AR
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --docdir="${EPREFIX}/usr/share/doc/${PF}"
+ $(use_enable openmp)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
new file mode 100644
index 000000000000..300868f52b76
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 5c6cb92..b99bedd 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+
+ # Checks for header files.
+ AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
new file mode 100644
index 000000000000..42066f7f2152
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 506ea0c..a0a403c 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -15,6 +15,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+
+ using namespace std;
+
diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
new file mode 100644
index 000000000000..c2cc35c31d98
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 1a169cf..36cc05b 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -16,6 +16,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+
+ using namespace std;
+
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
new file mode 100644
index 000000000000..158e9b1262e4
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
+
diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
new file mode 100644
index 000000000000..c2cc35c31d98
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 1a169cf..36cc05b 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -16,6 +16,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+
+ using namespace std;
+
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
new file mode 100644
index 000000000000..8209935b6d9e
--- /dev/null
+++ b/sci-biology/allpathslg/Manifest
@@ -0,0 +1,3 @@
+DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
+DIST allpathslg-47093.tar.gz 3057279 SHA256 493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512 499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314 WHIRLPOOL a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc
+DIST allpathslg-52415.tar.gz 3129266 SHA256 3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512 afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6 WHIRLPOOL de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785
diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild b/sci-biology/allpathslg/allpathslg-42337.ebuild
new file mode 100644
index 000000000000..9fb44dfcc905
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-42337.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 -x86"
+
+DEPEND="
+ dev-libs/boost
+ !sci-biology/allpaths
+ sci-biology/vaal"
+RDEPEND=""
+
+src_prepare() {
+ sed -i 's/-ggdb3//' configure.ac || die
+ eautoreconf
+}
+
+src_install() {
+ einstall || die
+ # Provided by sci-biology/vaal
+ for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
+ rm "${D}/usr/bin/$i" || die
+ done
+}
diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild b/sci-biology/allpathslg/allpathslg-47093.ebuild
new file mode 100644
index 000000000000..ab971ec46c89
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-47093.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 -x86"
+
+DEPEND="
+ dev-libs/boost
+ !sci-biology/allpaths
+ sci-biology/vaal"
+RDEPEND=""
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc4.9.patch
+ sed -i 's/-ggdb//' configure.ac || die
+ eautoreconf
+}
+
+src_install() {
+ default
+ # Provided by sci-biology/vaal
+ for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
+ rm "${ED}/usr/bin/$i" || die
+ done
+}
diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild
new file mode 100644
index 000000000000..29de20e37670
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-52415.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="openmp"
+
+DEPEND="
+ dev-libs/boost
+ !sci-biology/allpaths
+ sci-biology/vaal"
+RDEPEND=""
+
+pkg_pretend() {
+ # as of release 44849, GCC 4.7.0 (or higher) is required
+ # seems pre gcc-4.7 users must stay with:
+ # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \
+ die "You need to use gcc >4.7"
+ fi
+}
+
+src_prepare() {
+ local i
+ sed \
+ -e 's/-ggdb//' \
+ -e 's:CEHCK:CHECK:g' \
+ -i configure.ac || die
+ for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
+ sed -e "/bin_PROGRAMS/s: ${i} : :g" -i src/Makefile.am || die
+ done
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable openmp)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch
new file mode 100644
index 000000000000..46e5493d28ce
--- /dev/null
+++ b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch
@@ -0,0 +1,16 @@
+ src/paths/long/VariantCallTools.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/paths/long/VariantCallTools.cc b/src/paths/long/VariantCallTools.cc
+index dfe2787..725878b 100644
+--- a/src/paths/long/VariantCallTools.cc
++++ b/src/paths/long/VariantCallTools.cc
+@@ -1674,7 +1674,7 @@ void EdgesOnRef::FindAllPathsNoLoop(const GraphT& dg, int entrace_edge, int exit
+ int n1 = to_right2[entrace_edge];
+ int n2 = to_left2[exit_edge];
+
+- PartialPath start = {{n1},{}};
++ PartialPath start{{n1},vec<int>{}};
+ stack<PartialPath> visited;
+ visited.push(start);
+ while (! visited.empty()) {
diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/allpathslg/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
new file mode 100644
index 000000000000..35e082de93b9
--- /dev/null
+++ b/sci-biology/amap/Manifest
@@ -0,0 +1 @@
+DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4
diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild
new file mode 100644
index 000000000000..389102a8e757
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2
+
+MY_P=${PN}.${PV}
+
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+RDEPEND="java? ( >=virtual/jre-1.5 )"
+DEPEND="java? ( >=virtual/jdk-1.5 )"
+
+S=${WORKDIR}/${PN}-align
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-makefile.patch \
+ "${FILESDIR}"/${P}-includes.patch
+}
+
+src_compile() {
+ emake -C align CXX="$(tc-getCXX)" \
+ OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed"
+
+ if use java; then
+ pushd "${S}"/display
+ eant -Ddisplay all || die
+ popd
+ fi
+}
+
+src_install() {
+ dobin align/${PN} || die
+ dodoc align/{README,PROBCONS.README} || die
+ insinto /usr/share/${PN}/examples
+ doins examples/* || die
+ if use java; then
+ java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
+ java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
+ fi
+}
diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch
new file mode 100644
index 000000000000..77c4261db5cf
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-includes.patch
@@ -0,0 +1,44 @@
+Fixes build with gcc 4.3 and 4.6
+
+http://bugs.gentoo.org/217921
+http://bugs.gentoo.org/360517
+
+--- amap-align/align/Amap.cc
++++ amap-align/align/Amap.cc
+@@ -12,6 +12,8 @@
+ #include "ProbabilisticModel.h"
+ #include "EvolutionaryTree.h"
+ #include "SparseMatrix.h"
++#include <limits>
++#include <climits>
+ #include <string>
+ #include <sstream>
+ #include <iomanip>
+@@ -23,6 +25,7 @@
+ #include <cstdlib>
+ #include <cerrno>
+ #include <iomanip>
++#include <cstring>
+
+ string parametersInputFilename = "";
+ string parametersOutputFilename = "no training";
+--- amap-align/align/MultiSequenceDag.h
++++ amap-align/align/MultiSequenceDag.h
+@@ -13,6 +13,7 @@
+ #include <map>
+ #include <queue>
+ #include <iostream>
++#include <limits>
+ #include "MultiSequence.h"
+ #include "SparseMatrix.h"
+
+--- amap-align/align/SafeVector.h.org 2011-03-26 11:50:11.935069583 +0100
++++ amap-align/align/SafeVector.h 2011-03-26 11:50:21.112553151 +0100
+@@ -9,6 +9,7 @@
+ #define SAFEVECTOR_H
+
+ #include <cassert>
++#include <cstddef>
+ #include <vector>
+
+ /////////////////////////////////////////////////////////////////
diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch
new file mode 100644
index 000000000000..5a9841c98255
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-makefile.patch
@@ -0,0 +1,35 @@
+Respect {CXX,LD}FLAGS
+
+http://bugs.gentoo.org/332009
+
+--- amap-align/align/Makefile
++++ amap-align/align/Makefile
+@@ -15,6 +15,8 @@
+ # c) RELEASE mode
+ ################################################################################
+
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"'
+
+ # debug mode
+@@ -26,8 +28,7 @@
+
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+-
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+ ################################################################################
+ # 3) Dependencies
+ ################################################################################
+
+@@ -38,7 +37,7 @@
+ all : $(TARGETS)
+
+ amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc
+- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm
+
+ .PHONY : clean
+ clean:
diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml
new file mode 100644
index 000000000000..34294c65ca04
--- /dev/null
+++ b/sci-biology/amap/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
new file mode 100644
index 000000000000..27ad50ff28ed
--- /dev/null
+++ b/sci-biology/amos/Manifest
@@ -0,0 +1 @@
+DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61
diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild
new file mode 100644
index 000000000000..a4c860bdbe7f
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils python-r1
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt4"
+
+DEPEND="qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+ dev-perl/DBI
+ dev-perl/Statistics-Descriptive
+ sci-biology/mummer"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch \
+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+}
+
+src_install() {
+ default
+ python_replicate_script "${ED}"/usr/bin/goBambus2
+}
diff --git a/sci-biology/amos/amos-3.1.0.ebuild b/sci-biology/amos/amos-3.1.0.ebuild
new file mode 100644
index 000000000000..945ec9f41b4c
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="qt4"
+
+DEPEND="qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+ dev-perl/DBI
+ dev-perl/Statistics-Descriptive
+ sci-biology/mummer"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+}
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
new file mode 100644
index 000000000000..de2a41184c52
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/Align/find-tandem.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
+index ddf1cab..a29e21e 100644
+--- a/src/Align/find-tandem.cc
++++ b/src/Align/find-tandem.cc
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <ctime>
+ #include <sys/time.h>
++#include <unistd.h>
+ using namespace std;
+
+ const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
new file mode 100644
index 000000000000..97a8f59d0208
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
@@ -0,0 +1,25 @@
+--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200
++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200
+@@ -1,7 +1,7 @@
+ #pipeline script for assembly + Bambus 2
+ #contributed by Todd J Treangen
+
+-import string, sys, os, subprocess#, spincursor
++import sys, os, subprocess#, spincursor
+
+ RED = "\033[0;31m"
+ GREEN = "\033[0;32m"
+@@ -360,7 +360,7 @@
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+
+- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
+
+ if xopt_dict["verbose"] == 1:
+ print "10) running OutputResults"
+@@ -388,4 +388,3 @@
+ else:
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+-)
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
new file mode 100644
index 000000000000..a73ee9189a98
--- /dev/null
+++ b/sci-biology/amos/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">amos</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
new file mode 100644
index 000000000000..7ec0fa4e73a4
--- /dev/null
+++ b/sci-biology/arb/Manifest
@@ -0,0 +1,7 @@
+DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f
+DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43
+DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
+DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984
+DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583
+DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe
+DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
new file mode 100644
index 000000000000..7db2d798ec55
--- /dev/null
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+ http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+ mirror://gentoo/${P}-glibc2.10.patch.bz2
+ http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
+
+LICENSE="arb"
+SLOT="0"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ app-text/sablotron
+ media-libs/libpng
+ media-libs/tiff
+ www-client/lynx
+ x11-libs/libXaw
+ x11-libs/libXpm
+ x11-libs/motif:0
+ opengl? (
+ media-libs/glew
+ media-libs/freeglut
+ || (
+ media-libs/mesa[motif]
+ ( media-libs/mesa x11-libs/libGLw ) ) )"
+RDEPEND="${DEPEND}
+ sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+ unpack ${A}
+ mv arbsrc* ${P}
+}
+
+src_prepare() {
+ epatch \
+ "${WORKDIR}"/${P}-glibc2.10.patch\
+ "${WORKDIR}"/${P}-linker.patch \
+ "${FILESDIR}"/${PV}-libs.patch \
+ "${FILESDIR}"/${PV}-bfr-overflow.patch
+ sed -i \
+ -e 's/all: checks/all:/' \
+ -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+ -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+ -e 's/--export-dynamic/-Wl,--export-dynamic/g' \
+ "${S}/Makefile" || die
+ cp config.makefile.template config.makefile
+ sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+ use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+ use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+ emake ARBHOME="${S}" links || die
+}
+
+src_compile() {
+ emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die
+ use amd64 && mv arb.tgz arb.64.gentoo.tgz
+ use x86 && mv arb.tgz arb.32.gentoo.tgz
+ ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+ ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+ cat <<- EOF > "${S}/99${PN}"
+ ARBHOME=/opt/arb
+ PATH=/opt/arb/bin
+ LD_LIBRARY_PATH=/opt/arb/lib
+ EOF
+ doenvd "${S}/99${PN}" || die
+}
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
new file mode 100644
index 000000000000..97f7dc5dfbdd
--- /dev/null
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+ http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+ http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+ media-libs/libpng
+ media-libs/tiff
+ www-client/lynx
+ x11-libs/libXaw
+ x11-libs/libXpm
+ x11-libs/motif:0
+ opengl? (
+ media-libs/glew
+ media-libs/freeglut
+ || (
+ media-libs/mesa[motif]
+ ( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+ sys-process/time"
+RDEPEND="${CDEPEND}
+ sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+ unpack ${A}
+ mv arbsrc* ${P}
+}
+
+src_prepare() {
+ epatch \
+ "${WORKDIR}"/${P}-linker.patch \
+ "${FILESDIR}"/5.1-libs.patch \
+ "${FILESDIR}"/5.1-bfr-overflow.patch \
+ "${FILESDIR}"/${PV}-libpng15.patch \
+ "${FILESDIR}"/${P}-gcc-47.patch
+ sed \
+ -e 's/all: checks/all:/' \
+ -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+ -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+ -e 's:-O4::g' \
+ -e 's:-pipe::g' \
+ -i "${S}/Makefile" || die
+ cp config.makefile.template config.makefile
+ sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+ use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+ use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+ emake ARBHOME="${S}" links
+}
+
+src_compile() {
+ emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+ use amd64 && mv arb.tgz arb.64.gentoo.tgz
+ use x86 && mv arb.tgz arb.32.gentoo.tgz
+ ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+ ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+ cat <<- EOF > "${S}/99${PN}"
+ ARBHOME=/opt/arb
+ PATH=/opt/arb/bin
+ LD_LIBRARY_PATH=/opt/arb/lib
+ EOF
+ doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
new file mode 100644
index 000000000000..97f8b78ddca2
--- /dev/null
+++ b/sci-biology/arb/arb-5.3.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+ http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+ http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+ media-libs/libpng
+ media-libs/tiff
+ www-client/lynx
+ x11-libs/libXaw
+ x11-libs/libXpm
+ x11-libs/motif:0
+ opengl? (
+ media-libs/glew
+ media-libs/freeglut
+ || (
+ media-libs/mesa[motif]
+ ( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+ sys-process/time"
+RDEPEND="${CDEPEND}
+ sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+ unpack ${A}
+ mv arbsrc* ${P}
+}
+
+src_prepare() {
+ epatch \
+ "${WORKDIR}"/${P}-linker.patch \
+ "${FILESDIR}"/5.1-libs.patch \
+ "${FILESDIR}"/5.1-bfr-overflow.patch \
+ "${FILESDIR}"/5.2-libpng15.patch \
+ "${FILESDIR}"/${PN}-5.2-gcc-47.patch
+ sed \
+ -e 's/all: checks/all:/' \
+ -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+ -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+ -i "${S}/Makefile" || die
+ cp config.makefile.template config.makefile
+ sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+ use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+ use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+ emake ARBHOME="${S}" links
+}
+
+src_compile() {
+ emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+ use amd64 && mv arb.tgz arb.64.gentoo.tgz
+ use x86 && mv arb.tgz arb.32.gentoo.tgz
+ ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+ ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+ cat <<- EOF > "${S}/99${PN}"
+ ARBHOME=/opt/arb
+ PATH=/opt/arb/bin
+ LD_LIBRARY_PATH=/opt/arb/lib
+ EOF
+ doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch
new file mode 100644
index 000000000000..21d21f5ac17f
--- /dev/null
+++ b/sci-biology/arb/files/5.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ ARB_GDE/GDE_HGLfile.cxx | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx
+index e353a89..f69635a 100644
+--- a/ARB_GDE/GDE_HGLfile.cxx
++++ b/ARB_GDE/GDE_HGLfile.cxx
+@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type)
+ if(this_elem->id[0] == '\0')
+ strncpy(this_elem->id,uniqueID(),79);
+ if(this_elem->short_name[0] == '\0')
+- strncpy(this_elem->short_name,this_elem->id,79);
++ strncpy(this_elem->short_name,this_elem->id,31);
+ if(this_elem->seqlen == 0)
+ this_elem->protect=
+ PROT_BASE_CHANGES+
diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch
new file mode 100644
index 000000000000..bf0bacad3286
--- /dev/null
+++ b/sci-biology/arb/files/5.1-libs.patch
@@ -0,0 +1,16 @@
+diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl
+index b653a66..b346c96 100644
+--- a/SOURCE_TOOLS/provide_libs.pl
++++ b/SOURCE_TOOLS/provide_libs.pl
+@@ -118,11 +118,6 @@ sub provide_libs($$$) {
+ foreach my $lib (keys %needed_by) {
+ update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir);
+ }
+- if ($opengl==1) {
+- foreach my $lib (keys %needed_by_opengl) {
+- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir);
+- }
+- }
+ }
+
+ sub main() {
diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch
new file mode 100644
index 000000000000..3d750e76efe3
--- /dev/null
+++ b/sci-biology/arb/files/5.2-libpng15.patch
@@ -0,0 +1,45 @@
+Fix building with libpng-1.5
+
+https://bugs.gentoo.org/show_bug.cgi?id=378353
+
+Patch written by Samuli Suominen <ssuominen@gentoo.org>
+--- a/GL/glpng/glpng.c
++++ b/GL/glpng/glpng.c
+@@ -285,7 +285,7 @@
+ endinfo = png_create_info_struct(png);
+
+ // DH: added following lines
+- if (setjmp(png->jmpbuf))
++ if (setjmp(png_jmpbuf(png)))
+ {
+ png_destroy_read_struct(&png, &info, &endinfo);
+ return 0;
+@@ -390,7 +390,7 @@
+ endinfo = png_create_info_struct(png);
+
+ // DH: added following lines
+- if (setjmp(png->jmpbuf))
++ if (setjmp(png_jmpbuf(png)))
+ {
+ png_destroy_read_struct(&png, &info, &endinfo);
+ return 0;
+@@ -569,7 +569,7 @@
+ #define ALPHA *q
+
+ switch (trans) {
+- case PNG_CALLBACK:
++ case PNG_CALLBACKT:
+ FORSTART
+ ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b);
+ FOREND
+--- a/GL/glpng/glpng.h
++++ b/GL/glpng/glpng.h
+@@ -57,7 +57,7 @@
+ #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS
+
+ /* Transparency parameters */
+-#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */
++#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */
+ #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */
+ #define PNG_SOLID -1 /* No transparency */
+ #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */
diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch
new file mode 100644
index 000000000000..186e78e450b3
--- /dev/null
+++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch
@@ -0,0 +1,15 @@
+ AWTI/AWTI_import.cxx | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx
+index 8e730ac..e3f9ff4 100644
+--- a/AWTI/AWTI_import.cxx
++++ b/AWTI/AWTI_import.cxx
+@@ -12,6 +12,7 @@
+ #include <GEN.hxx>
+
+ #include <climits>
++#include <unistd.h>
+
+ using namespace std;
+
diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/arb/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest
new file mode 100644
index 000000000000..a4bf86d55d3c
--- /dev/null
+++ b/sci-biology/ariadne/Manifest
@@ -0,0 +1 @@
+DIST ariadne-1.3.tar.Z 69427 SHA256 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289 WHIRLPOOL 460d8acf2bb49e097a9544ecc089ca60c3478b64ab4d903bd6ee801eccd62fc560bdccf1454c9f22632081cbf1df35de09a4f81d6c131d3f52f36753bc692927
diff --git a/sci-biology/ariadne/ariadne-1.3-r1.ebuild b/sci-biology/ariadne/ariadne-1.3-r1.ebuild
new file mode 100644
index 000000000000..80a05b612ca9
--- /dev/null
+++ b/sci-biology/ariadne/ariadne-1.3-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="Protein sequences and profiles comparison"
+
+HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
+SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z"
+
+LICENSE="ARIADNE"
+SLOT="0"
+KEYWORDS="~amd64 x86"
+IUSE=""
+
+DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/SRC-${PV}"
+
+src_unpack(){
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-gcc4.patch
+ sed -e "s/CC = gcc/CC = $(tc-getCC)/" \
+ -e "s/OPTIMISE = -O2/OPTIMISE = ${CFLAGS}/" \
+ -i Makefile || die
+ sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
+}
+
+src_install() {
+ dobin Linux/{ariadne,prospero} || die
+ dolib Linux/libseq.a || die
+ insinto /usr/include/${PN}
+ doins Include/*.h || die
+ dodoc README || die
+}
diff --git a/sci-biology/ariadne/ariadne-1.3-r2.ebuild b/sci-biology/ariadne/ariadne-1.3-r2.ebuild
new file mode 100644
index 000000000000..1fa55ce322db
--- /dev/null
+++ b/sci-biology/ariadne/ariadne-1.3-r2.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Protein sequences and profiles comparison"
+HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
+SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z"
+
+LICENSE="ARIADNE"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SRC-${PV}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc4.patch \
+ "${FILESDIR}"/${P}-implicits.patch
+ sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045
+ sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
+}
+
+src_compile() {
+ emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}"
+}
+
+src_install() {
+ dobin Linux/{ariadne,prospero}
+ use static-libs && dolib.a Linux/libseq.a
+ insinto /usr/include/${PN}
+ doins Include/*.h || die
+ dodoc README || die
+}
diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
new file mode 100644
index 000000000000..0192efd4db5e
--- /dev/null
+++ b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
@@ -0,0 +1,10 @@
+--- cl.c.old 2006-09-12 17:13:02.000000000 -0400
++++ cl.c 2006-09-12 17:13:34.000000000 -0400
+@@ -658,6 +658,7 @@
+ fclose(fp);
+ if ( ! stat( filename, &buf ) )
+ {
++ char *ctime(), *t;
+ sprintf( date, "%s", ctime(&buf.st_mtime) );
+ t = date;
+ while ( *t )
diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
new file mode 100644
index 000000000000..31c442b12265
--- /dev/null
+++ b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
@@ -0,0 +1,23 @@
+topalign.c:96:5: warning: implicit declaration of function ‘toupper’
+prospero.c:63:3: warning: implicit declaration of function ‘strcpy’
+
+--- SRC-1.3/prospero.c
++++ SRC-1.3/prospero.c
+@@ -26,6 +26,7 @@
+ */
+
+ #include<stdio.h>
++#include<string.h>
+ #include<math.h>
+ #include"cl.h"
+ #include"seq_util.h"
+--- SRC-1.3/topalign.c
++++ SRC-1.3/topalign.c
+@@ -26,6 +26,7 @@
+ */
+
+ #include<stdio.h>
++#include<ctype.h>
+ #include<math.h>
+ #include"seq_util.h"
+ #include"ariadne.h"
diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
new file mode 100644
index 000000000000..3e55c00f9d7b
--- /dev/null
+++ b/sci-biology/ariadne/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ ARIADNE is a package of two programs, ariadne and prospero, that
+ compare protein sequences and profiles using the Smith-Waterman
+ algorithm, and assesses statistical significance using a new accurate
+ formula, described in Mott, 2000, "Accurate Formula for P-values of
+ gapped local sequence and profile alignments" J. Mol Biol. 300:649-659.
+ The sequence/profile comparison algorithms used in ARIADNE are
+ standard, and are probably not the fastest implementations available.
+ The novel part is the method for determining statistical significance,
+ which will give thresholds of significance that are accurate to within
+ 5% 95% of the time.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
new file mode 100644
index 000000000000..cdfb577937e0
--- /dev/null
+++ b/sci-biology/augustus/Manifest
@@ -0,0 +1 @@
+DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild
new file mode 100644
index 000000000000..e58be6db6d6a
--- /dev/null
+++ b/sci-biology/augustus/augustus-2.5.5.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://augustus.gobics.de/"
+SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="examples"
+
+S="${WORKDIR}/${PN}.${PV}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-sane-build.patch
+ tc-export CC CXX
+}
+
+src_compile() {
+ emake clean && emake
+}
+
+src_install() {
+ dobin bin/*
+# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
+
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*.p*
+ insinto /usr/libexec/${PN}
+ doins scripts/*.conf
+
+ insinto /usr/share/${PN}
+ doins -r config
+
+ echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+
+ dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
+
+ if use examples; then
+ insinto /usr/share/${PN}/
+ doins -r docs/tutorial examples
+ fi
+}
diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
new file mode 100644
index 000000000000..39cd0762b1c1
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
@@ -0,0 +1,156 @@
+ Makefile | 8 +++---
+ scripts/Makefile | 6 +++-
+ scripts/aln2wig/Makefile | 8 +++---
+ scripts/compileSpliceCands/Makefile | 6 ++--
+ src/Makefile | 43 ++++++++++++++++++----------------
+ 5 files changed, 38 insertions(+), 33 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e23a667..64610c8 100644
+--- a/Makefile
++++ b/Makefile
+@@ -3,9 +3,9 @@
+ #
+
+ all:
+- cd src && ${MAKE}
+- cd scripts && ${MAKE}
++ $(MAKE) -C src
++ $(MAKE) -C scripts
+
+ clean:
+- cd src && ${MAKE} clean
+- cd scripts && ${MAKE} clean
++ $(MAKE) -C src clean
++ $(MAKE) -C scripts clean
+diff --git a/scripts/Makefile b/scripts/Makefile
+index 6d4dd67..ab6a885 100644
+--- a/scripts/Makefile
++++ b/scripts/Makefile
+@@ -1,5 +1,7 @@
+ all :
+- cd aln2wig && ${MAKE}
++ $(MAKE) -C aln2wig
++ $(MAKE) -C compileSpliceCands
+
+ clean :
+- cd aln2wig && ${MAKE} clean
++ $(MAKE) -C aln2wig clean
++ $(MAKE) -C compileSpliceCands
+diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
+index 64d09f5..9752980 100644
+--- a/scripts/aln2wig/Makefile
++++ b/scripts/aln2wig/Makefile
+@@ -1,10 +1,10 @@
+-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
+
+ psl2wig : aln2wig.o
+- gcc $(CFLAGS) -o aln2wig aln2wig.o;
+- cp aln2wig ../../bin
++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
++ cp aln2wig ../../bin/
+ psl2wig.o : aln2wig.c
+- gcc $(CFLAGS) -c aln2wig.c
++ $(CC) $(CFLAGS) -c aln2wig.c
+
+ all : psl2wig
+
+diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
+index cddada5..8079791 100644
+--- a/scripts/compileSpliceCands/Makefile
++++ b/scripts/compileSpliceCands/Makefile
+@@ -1,8 +1,8 @@
+ compileSpliceCands : compileSpliceCands.o list.h list.o
+- gcc -o compileSpliceCands compileSpliceCands.o list.o;
+-# cp compileSpliceCands ../../bin
++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
++ cp compileSpliceCands ../../bin/
+ compileSpliceCands.o : compileSpliceCands.c
+- gcc -Wall -pedantic -ansi -c compileSpliceCands.c
++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c
+
+ all : compileSpliceCands
+
+diff --git a/src/Makefile b/src/Makefile
+index 71795b6..732b953 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,8 +6,8 @@
+ # a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
+ # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
+ #
+-CC = g++
+-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static
++CXX ?= g++
++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static
+ INCLS = -I../include -I.
+ LIBS = # -lcwd
+ OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
+@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
+ PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
+ INFO = cflags
+
+-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
+
+ .SUFFIXES:
+ .SUFFIXES: .cc .o .so
+
+ .cc.o:
+- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
+
+-augustus: augustus.cc $(OBJS) $(DUMOBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++bin: $(PROGR)
++ cp $(PROGR) ../bin/
++
++augustus: augustus.o $(OBJS) $(DUMOBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp augustus ../bin/
+
+-etraining: etraining.cc $(TOBJS) $(OBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++etraining: etraining.o $(TOBJS) $(OBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp etraining ../bin/
+
+-evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++evaluate: evaluate.o $(OBJS) $(DUMOBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-consensusFinder: consensusFinder.cc consensus.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++consensusFinder: consensusFinder.o consensus.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-curve2hints: curve2hints.cc exon_seg.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++curve2hints: curve2hints.o exon_seg.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
+ types.o properties.o geneticcode.o pp_profile.o lldouble.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp fastBlockSearch ../bin/
+
+-prepareAlign: pp_prepare_align.cc
+- $(CC) $(CFLAGS) -o $@ $^
++prepareAlign: pp_prepare_align.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
+ cp prepareAlign ../bin/
+
+ info:
+- echo "$(CFLAGS)" > $(INFO)
++ echo "$(CXXFLAGS)" > $(INFO)
+
+ clean:
+- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/*
+
+ tidy: clean
+ rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/augustus/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
new file mode 100644
index 000000000000..1c1972c599d5
--- /dev/null
+++ b/sci-biology/bamtools/Manifest
@@ -0,0 +1,2 @@
+DIST bamtools-1.0.2.tar.gz 207523 SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512 1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244 WHIRLPOOL 9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990
+DIST bamtools-2.3.0.tar.gz 539446 SHA256 288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af SHA512 432f66384cffc04ab6bc7dc66d8f7b79c1e468d0068db4cabb5cac05f9b6bef7968eff71ffb3ee51b84e23d9bb66a11ef267024138f40116c25e7f18e7210a5c WHIRLPOOL dd888f67c3d0b0ce2f5f2875e242e5df0d54cefd13693230b5f10eb57dd780304b601027cf65f6598a54061a7166903bf06c6c9a46939f6ce6bbb246cab89993
diff --git a/sci-biology/bamtools/bamtools-1.0.2.ebuild b/sci-biology/bamtools/bamtools-1.0.2.ebuild
new file mode 100644
index 000000000000..08c40d0705d3
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-1.0.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+SRC_URI="mirror://github/pezmaster31/bamtools/"${P}".tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ for i in bin/bamtools-${PV} lib/libbamtools.so.${PV} lib/libbamtools-utils.so.${PV}; do
+ TMPDIR="$(pwd)" scanelf -Xr $i || die
+ done
+
+ dobin bin/bamtools
+ dolib lib/*
+ insinto /usr/include/bamtools/api
+ doins include/api/*
+ insinto /usr/include/bamtools/shared
+ doins include/shared/*
+ dodoc README
+}
diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild b/sci-biology/bamtools/bamtools-2.3.0.ebuild
new file mode 100644
index 000000000000..cb86750cc0cf
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.3.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ >=dev-libs/jsoncpp-0.5.0-r1
+ sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-unbundle.patch )
+
+src_install() {
+ cmake-utils_src_install
+ use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a
+}
diff --git a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
new file mode 100644
index 000000000000..318396e75c36
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
@@ -0,0 +1,32 @@
+ src/CMakeLists.txt | 1 -
+ src/api/CMakeLists.txt | 4 ++--
+ src/toolkit/bamtools_filter.cpp | 2 +-
+ 3 files changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index e359695..2bd2185 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -6,7 +6,6 @@
+ # ==========================
+
+ add_subdirectory( api )
+-add_subdirectory( third_party )
+ add_subdirectory( toolkit )
+ add_subdirectory( utils )
+
+diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
+index 66eb35f..65f4639 100644
+--- a/src/api/CMakeLists.txt
++++ b/src/api/CMakeLists.txt
+@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} )
+ target_link_libraries( BamTools-static ${APILibs} )
+
+ # set library install destinations
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}")
+
+ # export API headers
+ include(../ExportHeader.cmake)
diff --git a/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch
new file mode 100644
index 000000000000..c07c59d2cddd
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch
@@ -0,0 +1,23 @@
+--- bamtools-2.3.0/src/api/CMakeLists.txt.ori 2013-08-27 18:00:43.000000000 +0200
++++ bamtools-2.3.0/src/api/CMakeLists.txt 2013-08-27 18:00:47.000000000 +0200
+@@ -54,8 +54,8 @@
+ target_link_libraries( BamTools-static ${APILibs} )
+
+ # set library install destinations
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}")
+
+ # export API headers
+ include(../ExportHeader.cmake)
+--- bamtools-2.3.0/src/CMakeLists.txt.ori 2013-08-27 18:03:10.000000000 +0200
++++ bamtools-2.3.0/src/CMakeLists.txt 2013-08-27 18:03:23.000000000 +0200
+@@ -6,7 +6,6 @@
+ # ==========================
+
+ add_subdirectory( api )
+-add_subdirectory( third_party )
+ add_subdirectory( toolkit )
+ add_subdirectory( utils )
+
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
new file mode 100644
index 000000000000..f2c00c1fdd0c
--- /dev/null
+++ b/sci-biology/bamtools/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <herd>proxy-maintainers</herd>
+ <maintainer>
+ <email>mmokrejs@gmail.com</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
+ <upstream>
+ <remote-id type="github">pezmaster31/bamtools</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
new file mode 100644
index 000000000000..7fd843d7d423
--- /dev/null
+++ b/sci-biology/beast-mcmc/Manifest
@@ -0,0 +1,2 @@
+DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a
+DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
new file mode 100644
index 000000000000..d25ed786a751
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
+
+WANT_ANT_TASKS="ant-junit4"
+EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+JAVA_ANT_ENCODING="latin1"
+JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
+
+#inherit java-pkg-2 java-ant-2 eutils subversion
+inherit java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
+HOMEPAGE="http://code.google.com/p/beast-mcmc/"
+#SRC_URI=""
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# TODO: sys-cluster/mpijava
+COMMON_DEPS="dev-java/colt:0
+ dev-java/jdom:1.0
+ dev-java/itext:0
+ dev-java/junit:4
+ dev-java/jebl:0
+ dev-java/matrix-toolkits-java
+ dev-java/commons-math:2
+ dev-java/jdom-jaxen:1.0"
+DEPEND=">=virtual/jdk-1.5
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.5
+ ${COMMON_DEPS}"
+
+S="${WORKDIR}/beast_release_${PV//./_}"
+
+src_prepare() {
+ sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
+ cd lib
+ rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
+ java-pkg_jar-from jdom-1.0
+ java-pkg_jar-from colt
+ java-pkg_jar-from itext
+ java-pkg_jar-from jebl
+ java-pkg_jar-from matrix-toolkits-java
+ java-pkg_jar-from commons-math-1
+ java-pkg-2_src_prepare
+}
+
+src_compile() {
+ eant dist_all_BEAST -f build_BEAST_MCMC.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+ eant dist -f build_pathogen.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+}
+
+src_install() {
+ java-pkg_dojar build/dist/*.jar dist/*.jar
+
+ java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
+# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
+
+ insinto /usr/share/${PN}
+ doins -r examples || die
+ dodoc NOTIFY doc/*.pdf
+}
+
+src_test() {
+ eant junit -f build_BEAST_MCMC.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+}
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
new file mode 100644
index 000000000000..35993562814c
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
+
+WANT_ANT_TASKS="ant-junit4"
+EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+JAVA_ANT_ENCODING="latin1"
+JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
+
+#inherit java-pkg-2 java-ant-2 eutils subversion
+inherit java-pkg-2 java-ant-2 eutils
+
+MY_P=BEASTv${PV}
+
+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
+HOMEPAGE="http://code.google.com/p/beast-mcmc/"
+#SRC_URI=""
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# TODO: sys-cluster/mpijava
+COMMON_DEPS="
+ dev-java/colt:0
+ dev-java/jdom:1.0
+ dev-java/itext:0
+ dev-java/junit:4
+ dev-java/jebl:0
+ dev-java/matrix-toolkits-java
+ dev-java/commons-math:2
+ dev-java/jdom-jaxen:1.0"
+DEPEND=">=virtual/jdk-1.5
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.5
+ ${COMMON_DEPS}"
+
+S="${WORKDIR}/beast_release_${PV//./_}"
+
+src_prepare() {
+ sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die
+ cd lib
+ rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die
+ #rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
+ java-pkg_jar-from jdom-1.0
+ java-pkg_jar-from colt
+ java-pkg_jar-from itext
+# java-pkg_jar-from jebl
+ java-pkg_jar-from matrix-toolkits-java
+ java-pkg_jar-from commons-math-2
+ java-pkg-2_src_prepare
+}
+
+src_compile() {
+ eant dist_all_BEAST -f build_BEAST_MCMC.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+ eant dist -f build_pathogen.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+}
+
+src_install() {
+ java-pkg_dojar build/dist/*.jar dist/*.jar
+
+ java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
+# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
+
+ insinto /usr/share/${PN}
+ doins -r examples
+ dodoc NOTIFY doc/*.pdf
+}
+
+src_test() {
+ eant junit -f build.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done)
+}
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
new file mode 100644
index 000000000000..30c1a3751011
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
+
+WANT_ANT_TASKS="ant-junit4"
+EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+JAVA_ANT_ENCODING="latin1"
+JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
+
+inherit java-pkg-2 java-ant-2 eutils subversion
+
+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
+HOMEPAGE="http://code.google.com/p/beast-mcmc/"
+SRC_URI=""
+#SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# TODO: sys-cluster/mpijava
+COMMON_DEPS="dev-java/colt:0
+ dev-java/jdom:1.0
+ dev-java/itext:0
+ dev-java/junit:4
+ dev-java/jebl:0
+ dev-java/matrix-toolkits-java
+ dev-java/commons-math:2
+ dev-java/jdom-jaxen:1.0"
+DEPEND=">=virtual/jdk-1.5
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.5
+ ${COMMON_DEPS}"
+
+S="${WORKDIR}/beast_release_${PV//./_}"
+
+src_prepare() {
+ sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
+ cd lib
+ rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
+ java-pkg_jar-from jdom-1.0
+ java-pkg_jar-from colt
+ java-pkg_jar-from itext
+ java-pkg_jar-from jebl
+ java-pkg_jar-from matrix-toolkits-java
+ java-pkg_jar-from commons-math-1
+ java-pkg-2_src_prepare
+}
+
+src_compile() {
+ eant dist_all_BEAST -f build_BEAST_MCMC.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+ eant dist -f build_pathogen.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+}
+
+src_install() {
+ java-pkg_dojar build/dist/*.jar dist/*.jar
+
+ java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
+# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
+ java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
+
+ insinto /usr/share/${PN}
+ doins -r examples || die
+ dodoc NOTIFY doc/*.pdf
+}
+
+src_test() {
+ eant junit -f build_BEAST_MCMC.xml \
+ -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
+}
diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/beast-mcmc/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
new file mode 100644
index 000000000000..e8ecdb88e2ea
--- /dev/null
+++ b/sci-biology/bedtools/Manifest
@@ -0,0 +1,2 @@
+DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772
+DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84
diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild
new file mode 100644
index 000000000000..7de4f347c710
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.16.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/BEDTools-Version-${PV}"
+
+src_prepare() {
+ filter-ldflags -Wl,--as-needed
+ sed -i \
+ -e '/export CXXFLAGS/ d' \
+ -e '/export CXX/ d' \
+ Makefile || die
+}
+
+src_install() {
+ dobin bin/*
+ dodoc README* RELEASE_HISTORY
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild
new file mode 100644
index 000000000000..cdba954f6d27
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.20.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/bedtools2-${PV}"
+
+src_prepare() {
+ filter-ldflags -Wl,--as-needed
+ sed -i \
+ -e '/export CXXFLAGS/ d' \
+ -e '/export CXX/ d' \
+ Makefile || die
+}
+
+src_install() {
+ dobin bin/*
+ dodoc README* RELEASE_HISTORY
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
new file mode 100644
index 000000000000..6edffa4a6dc3
--- /dev/null
+++ b/sci-biology/bedtools/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <herd>proxy-maintainers</herd>
+ <maintainer>
+ <email>mmokrejs@gmail.com</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <longdescription>
+ BEDTools: a flexible suite of utilities for comparing genomic features.
+ </longdescription>
+ <upstream>
+ <remote-id type="google-code">bedtools</remote-id>
+ <remote-id type="github">arq5x/bedtools2</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest
new file mode 100644
index 000000000000..532e6e077652
--- /dev/null
+++ b/sci-biology/bfast/Manifest
@@ -0,0 +1 @@
+DIST bfast-0.7.0a.tar.gz 2456617 SHA256 ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 WHIRLPOOL f9098c00a2f328fd5116447aae86f0aed078f6c2e6a49a4459e09f0c2a2023e0d60be1893fc2337b85444c24efb2636953517eda2ced336d1bc6dc8d94706e6b
diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild
new file mode 100644
index 000000000000..908334354033
--- /dev/null
+++ b/sci-biology/bfast/bfast-0.7.0a.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Blat-like Fast Accurate Search Tool"
+HOMEPAGE="https://sourceforge.net/projects/bfast/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="test"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="dev-perl/XML-Simple"
+
+src_prepare() {
+ sed \
+ -e 's/-m64//' \
+ -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \
+ -e 's:-g -O2::g' \
+ -i configure.ac || die
+ sed \
+ -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \
+ -i tests/*sh || die
+
+ sed \
+ -e '/docdir/d' \
+ -i Makefile.am || die
+
+ use test && AUTOTOOLS_IN_SOURCE_BUILD=1
+
+ autotools-utils_src_prepare
+}
diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml
new file mode 100644
index 000000000000..45107864e217
--- /dev/null
+++ b/sci-biology/bfast/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">bfast</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest
new file mode 100644
index 000000000000..0bd1b4ccfa7a
--- /dev/null
+++ b/sci-biology/biogrep/Manifest
@@ -0,0 +1 @@
+DIST biogrep-1.0.tar.gz 71867 RMD160 8f22aaa432febbf7d433402ca5da1afe7a98a217 SHA1 b4c24777e94d9f04dfda0d2d6a4599e3bc470a4f SHA256 15421d79f6f16d6bf9bef132a97f7f9ede1bd42d3fb90572df04a1e1abd8cfd8
diff --git a/sci-biology/biogrep/biogrep-1.0-r1.ebuild b/sci-biology/biogrep/biogrep-1.0-r1.ebuild
new file mode 100644
index 000000000000..f4af74c73bff
--- /dev/null
+++ b/sci-biology/biogrep/biogrep-1.0-r1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit toolchain-funcs
+
+DESCRIPTION="Multithreading application for matching large sets of patternsagainst biosequence dbs"
+HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml"
+SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_prepare() {
+ tc-export CC
+}
+
+src_install() {
+ emake prefix="${D}"/usr install || die "install failed"
+ dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed"
+}
diff --git a/sci-biology/biogrep/biogrep-1.0.ebuild b/sci-biology/biogrep/biogrep-1.0.ebuild
new file mode 100644
index 000000000000..b2161dcaae5b
--- /dev/null
+++ b/sci-biology/biogrep/biogrep-1.0.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Multithreading application for matching large sets of patterns
+against biosequence dbs."
+HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml"
+SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_install() {
+ emake prefix="${D}"/usr install || die "install failed"
+ dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed"
+}
diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml
new file mode 100644
index 000000000000..173e3b48f53e
--- /dev/null
+++ b/sci-biology/biogrep/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+<maintainer>
+ <email>jlec@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
+
diff --git a/sci-biology/biojava/Manifest b/sci-biology/biojava/Manifest
new file mode 100644
index 000000000000..3a20f1c431f2
--- /dev/null
+++ b/sci-biology/biojava/Manifest
@@ -0,0 +1,2 @@
+DIST biojava-1.6-all.jar 24571007 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e SHA512 300bd6e02fe052c810c52cb2cc4255628bee704af187ad746b97e57941778dc3a1996b3917db021d74db8c716f94c90c94c5a5e2d4bc212c06259381045f3034 WHIRLPOOL e5a52aaa6e9a9d6780d5f55b6d164db07388e9c595296d4e4a11dc241aa0745fa726279d19a0c97d1966b0a14c06af2b9b588873ad522aeeff881534f0871f10
+DIST biojava-1.7-all.jar 28062592 SHA256 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SHA512 867862b45f014bcd1afd37691e91b948ede05e96f84c7051953d32dad49908781235aad80301e22a15fa8b4145e80c78cf3935d6e581a2e60b56c9308f8adaa8 WHIRLPOOL 5669293ce362e82562454c5902d523e69f64d90e117e75b5de844e0ef5866d250507b86f78245ac82f19932ad9aa196ad17d96a3f703187a3ab2daf00893af9b
diff --git a/sci-biology/biojava/biojava-1.6.ebuild b/sci-biology/biojava/biojava-1.6.ebuild
new file mode 100644
index 000000000000..edfadace1dcc
--- /dev/null
+++ b/sci-biology/biojava/biojava-1.6.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java framework for processing biological data"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+ dev-java/commons-cli:1
+ dev-java/commons-dbcp:0
+ dev-java/commons-pool:0
+ dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+ ${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+ app-arch/unzip
+ ${COMMON_DEPEND}
+ test?
+ (
+ dev-java/junit:4
+ dev-java/ant-junit4
+ )"
+
+S="${WORKDIR}/biojava-live_${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+ einfo "Removing budled jars."
+ find . -name "*.jar" -print -delete
+ rm -r doc/*
+ java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+ java-pkg_jar-from commons-cli-1
+ java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+ java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+ java-pkg_jar-from bytecode
+}
+
+src_compile() {
+ #ANT_OPTS="${ANT_OPTS} -Xmx512m"
+ eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+ java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+ java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+ java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+ #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+ use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+ java-pkg_jar-from junit-4 junit.jar junit-4.4.jar
+ ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/sci-biology/biojava/biojava-1.7.ebuild b/sci-biology/biojava/biojava-1.7.ebuild
new file mode 100644
index 000000000000..77ff74c2d159
--- /dev/null
+++ b/sci-biology/biojava/biojava-1.7.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java framework for processing biological data"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+ dev-java/commons-cli:1
+ dev-java/commons-dbcp:0
+ dev-java/commons-pool:0
+ dev-java/commons-collections:0
+ dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+ ${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+ app-arch/unzip
+ ${COMMON_DEPEND}
+ test?
+ (
+ dev-java/junit:4
+ dev-java/ant-junit4
+ )"
+
+S="${WORKDIR}/biojava-${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+ einfo "Removing bundled jars..."
+ find . -name "*.jar" -print -delete
+ java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+ java-pkg_jar-from commons-cli-1
+ java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+ java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+ java-pkg_jar-from bytecode
+}
+
+src_compile() {
+ #ANT_OPTS="${ANT_OPTS} -Xmx512m"
+ eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+ java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+ java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+ java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+ #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+ use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+ java-pkg_jar-from junit-4 junit.jar junit-4.4.jar
+ ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml
new file mode 100644
index 000000000000..0a18364544e8
--- /dev/null
+++ b/sci-biology/biojava/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <herd>java</herd>
+</pkgmetadata>
diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest
new file mode 100644
index 000000000000..b189a8ae405f
--- /dev/null
+++ b/sci-biology/bioperl-db/Manifest
@@ -0,0 +1 @@
+DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
new file mode 100644
index 000000000000..b78237d1e434
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-DB
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="test"
+SRC_TEST="do"
+
+CDEPEND="
+ >=sci-biology/bioperl-${PV}
+ dev-perl/DBD-mysql
+ dev-perl/DBI
+ sci-biology/biosql"
+DEPEND="${CDEPEND}
+ dev-perl/Module-Build"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
new file mode 100644
index 000000000000..aad5b6e4abe5
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module git-2
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="git://github.com/bioperl/${PN}.git
+ https://github.com/bioperl/${PN}.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+ dev-perl/DBI
+ sci-biology/biosql"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/BioPerl-db-${PV}"
+
+src_configure() {
+ # This disables tests. TODO: Enable tests
+ sed -i -e '/biosql_conf();/d' \
+ -e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die
+ perl-module_src_configure
+}
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml
new file mode 100644
index 000000000000..642468c809b7
--- /dev/null
+++ b/sci-biology/bioperl-db/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="cpan">BioPerl-DB</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest
new file mode 100644
index 000000000000..54877a23bece
--- /dev/null
+++ b/sci-biology/bioperl-network/Manifest
@@ -0,0 +1 @@
+DIST BioPerl-Network-1.006900.tar.gz 2198089 SHA256 5b31ab7d048ee8e7bd6ba933f96b904d7ee06b46ab29c00276eca3513a77c32a SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 WHIRLPOOL 65ff9e2509c0136232b7cff1aa5e8ad55f26241f51e70e6d34f9383c0af4bfdb0c5358b1a69075d480e9e1fdfa19342058fbe33ea4d4a633220ef3a80d6ed984
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
new file mode 100644
index 000000000000..285db499bff4
--- /dev/null
+++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-Network
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="test"
+SRC_TEST="do"
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+ >=dev-perl/Graph-0.86"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+ mydoc="AUTHORS BUGS"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild
new file mode 100644
index 000000000000..5b93a4ddbeed
--- /dev/null
+++ b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module git-2
+
+DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="git://github.com/bioperl/${PN}.git
+ https://github.com/bioperl/${PN}.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="test"
+SRC_TEST="do"
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+ >=dev-perl/Graph-0.86"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/BioPerl-network-${PV}"
+
+src_install() {
+ mydoc="AUTHORS BUGS"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml
new file mode 100644
index 000000000000..045af7cc6148
--- /dev/null
+++ b/sci-biology/bioperl-network/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="cpan">BioPerl-Network</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
new file mode 100644
index 000000000000..bd1970f7c390
--- /dev/null
+++ b/sci-biology/bioperl-run/Manifest
@@ -0,0 +1 @@
+DIST BioPerl-Run-1.006900.tar.gz 14546677 SHA256 6eddca8aae38a139caaa0b28505e2ff3e919e8ed39b7539a662b0145f1f08d96 SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c WHIRLPOOL a671180b3680d94683e771ba661e0f86430814200efcd8df1552dbc3c30228d90ea8be1b47cc36603cbfc6eadacb276414ae6d79e30ec80495fd836eb1732cca
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
new file mode 100644
index 000000000000..d633fe3be7a1
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-Run
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="-minimal test"
+#SRC_TEST="do"
+
+RESTRICT="test"
+
+CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE}
+ !minimal? (
+ dev-perl/Algorithm-Diff
+ dev-perl/XML-Twig
+ dev-perl/IO-String
+ dev-perl/IPC-Run
+ dev-perl/File-Sort
+ )"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+ # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
+ # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
+ #find "${D}" -name '*ConfigData*' -print -delete
+}
diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
new file mode 100644
index 000000000000..13c3ca1477da
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module git-2
+
+DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="git://github.com/bioperl/${PN}.git
+ https://github.com/bioperl/${PN}.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="-minimal test"
+#SRC_TEST="do"
+
+RESTRICT="test"
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+ !minimal? (
+ dev-perl/Algorithm-Diff
+ dev-perl/XML-Twig
+ dev-perl/IO-String
+ dev-perl/IPC-Run
+ )"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/BioPerl-run-${PV}"
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+ # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
+ # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
+ find "${D}" -name '*ConfigData*' -print -delete
+}
diff --git a/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff
new file mode 100644
index 000000000000..5683347a6b52
--- /dev/null
+++ b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff
@@ -0,0 +1,22 @@
+--- Makefile.PL.original 2003-09-28 23:33:16.000000000 -0400
++++ Makefile.PL 2003-09-28 23:33:50.000000000 -0400
+@@ -73,19 +73,6 @@
+ my $DISTNAME = "bioperl-run";
+ my $VERSION = "1.2.2";
+
+-my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n');
+-if( $proceed =~ /^[yY]/) {
+- my $address = prompt("Enter your email address (no default)",'');
+-
+- if (open T,">t/pise-email.test") {
+-print T "$address\n";
+-close T;
+- } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); }
+-} else {
+- if( -e "t/pise-email.test" ) {
+-unlink "t/pise-email.test";
+- }
+-}
+ #$do_autoload_finesse = 0;
+ #$NAME = 'Bio';
+ #$DISTNAME = "GFD";
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
new file mode 100644
index 000000000000..f8c7078a2813
--- /dev/null
+++ b/sci-biology/bioperl-run/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="cpan">BioPerl-Run</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
new file mode 100644
index 000000000000..756ab900c480
--- /dev/null
+++ b/sci-biology/bioperl/Manifest
@@ -0,0 +1 @@
+DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild
new file mode 100644
index 000000000000..afaa8236b5a2
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+MY_PN=BioPerl
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.6.901
+inherit perl-module
+
+SUBPROJECTS="+db +network +run"
+MIN_PV=$PV
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
+
+REQUIRED_USE="minimal? ( !graphviz )"
+
+CDEPEND="
+ dev-perl/libwww-perl
+ !minimal? (
+ dev-perl/Algorithm-Munkres
+ dev-perl/Array-Compare
+ dev-perl/yaml
+ dev-perl/Bio-ASN1-EntrezGene
+ dev-perl/Clone
+ dev-perl/Convert-Binary-C
+ dev-perl/Data-Stag
+ dev-perl/GD
+ dev-perl/Graph
+ >=dev-perl/HTML-Parser-3.60
+ dev-perl/List-MoreUtils
+ dev-perl/Math-Random
+ dev-perl/PostScript
+ dev-perl/set-scalar
+ dev-perl/SOAP-Lite
+ dev-perl/Sort-Naturally
+ dev-perl/Spreadsheet-ParseExcel
+ >=virtual/perl-Storable-2.05
+ >=dev-perl/SVG-2.26
+ >=dev-perl/SVG-Graph-0.01
+ dev-perl/URI
+ >=dev-perl/XML-DOM-XPath-0.13
+ dev-perl/XML-Parser
+ >=dev-perl/XML-SAX-0.15
+ dev-perl/XML-Simple
+ dev-perl/XML-Twig
+ >=dev-perl/XML-Writer-0.4
+ dev-perl/XML-DOM
+ dev-perl/XML-XPath
+ )
+ graphviz? ( dev-perl/GraphViz )
+ sqlite? ( dev-perl/DBD-SQLite )"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+ network? ( >=sci-biology/bioperl-network-${MIN_PV} )
+ run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
new file mode 100644
index 000000000000..1cf70db6b533
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module git-2
+
+SUBPROJECTS="+db +network +run"
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="git://github.com/${PN}/${PN}-live.git
+ https://github.com/${PN}/${PN}-live.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="-minimal graphviz ${SUBPROJECTS}"
+
+CDEPEND="
+ dev-perl/Data-Stag
+ dev-perl/libwww-perl
+ !minimal? (
+ dev-perl/Ace
+ dev-perl/Bio-ASN1-EntrezGene
+ dev-perl/Spreadsheet-ParseExcel
+ dev-perl/Spreadsheet-WriteExcel
+ >=dev-perl/XML-SAX-0.15
+ dev-perl/Graph
+ dev-perl/SOAP-Lite
+ dev-perl/Array-Compare
+ dev-perl/SVG
+ dev-perl/XML-Simple
+ dev-perl/XML-Parser
+ dev-perl/XML-Twig
+ >=dev-perl/HTML-Parser-3.60
+ >=dev-perl/XML-Writer-0.4
+ dev-perl/Clone
+ dev-perl/XML-DOM
+ dev-perl/set-scalar
+ dev-perl/XML-XPath
+ dev-perl/XML-DOM-XPath
+ dev-perl/Algorithm-Munkres
+ dev-perl/Data-Stag
+ dev-perl/Math-Random
+ dev-perl/PostScript
+ dev-perl/Convert-Binary-C
+ dev-perl/SVG-Graph
+ )
+ graphviz? ( dev-perl/GraphViz )"
+DEPEND="dev-perl/Module-Build
+ ${CDEPEND}"
+RDEPEND="${CDEPEND}"
+PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
+ db? ( >=sci-biology/bioperl-db-${PV} )
+ network? ( >=sci-biology/bioperl-network-${PV} )
+ run? ( >=sci-biology/bioperl-run-${PV} )"
+
+S="${WORKDIR}/BioPerl-${PV}"
+
+src_configure() {
+ sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
+ -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \
+ -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \
+ || die
+ if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
+ perl-module_src_configure
+}
+
+src_install() {
+ mydoc="AUTHORS BUGS FAQ"
+ perl-module_src_install
+}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
new file mode 100644
index 000000000000..210ba364d45f
--- /dev/null
+++ b/sci-biology/bioperl/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="run">Install sci-biology/bioperl-run</flag>
+ <flag name="network">Install sci-biology/bioperl-run</flag>
+ <flag name="db">Install sci-biology/bioperl-run</flag>
+ </use>
+ <upstream>
+ <remote-id type="cpan">BioPerl</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
new file mode 100644
index 000000000000..e835e2490342
--- /dev/null
+++ b/sci-biology/biopython/Manifest
@@ -0,0 +1 @@
+DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2
diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild
new file mode 100644
index 000000000000..9c23f0bd0635
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.65.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} pypy )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
+SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-python/matplotlib[$(python_gen_usedep 'python*')]
+ dev-python/networkx[$(python_gen_usedep 'python*')]
+ dev-python/numpy[$(python_gen_usedep 'python*')]
+ dev-python/rdflib[$(python_gen_usedep 'python*')]
+ dev-python/pygraphviz[$(python_gen_usedep 'python2*')]
+ dev-python/reportlab[$(python_gen_usedep 'python*')]
+ media-gfx/pydot[$(python_gen_usedep 'python2*')]
+ "
+DEPEND="${RDEPEND}
+ sys-devel/flex"
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch )
+
+python_test() {
+ [[ ${EPYTHON} == pypy ]] && return
+ cd Tests || die
+ ${PYTHON} run_tests.py || die
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+
+ dodir /usr/share/${PN}
+ cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
+}
+
+pkg_postinst() {
+ elog "For database support you need to install:"
+ optfeature "MySQL" dev-python/mysql-python
+ optfeature "PostGreSQL" dev-python/psycopg
+ echo
+ elog "Some applications need extra packages:"
+ optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}
diff --git a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch
new file mode 100644
index 000000000000..2efdef97d799
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch
@@ -0,0 +1,40 @@
+From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001
+From: Peter Cock <p.j.a.cock@googlemail.com>
+Date: Sun, 18 Jan 2015 02:07:54 +0000
+Subject: [PATCH] Clearer error message; update failing test.
+
+One of the orchid examples now returns different enough
+results that the test was failing. The new error message
+makes it much easier to pick another positive example to
+add to the the white-list.
+---
+ Tests/test_NCBI_qblast.py | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py
+index 88bfe61..19f7b35 100644
+--- a/Tests/test_NCBI_qblast.py
++++ b/Tests/test_NCBI_qblast.py
+@@ -66,7 +66,7 @@ def test_orchid_est(self):
+ AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA
+ GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA
+ ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""",
+- 0.0000001, None, ["21554275", "18409071", "296087288"])
++ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"])
+
+ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits):
+ try:
+@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_
+ print("Update this test to have some redundancy...")
+ for alignment in record.alignments:
+ print(alignment.hit_id)
+- assert found_result, "Missing all of %s in alignments" \
+- % ", ".join(expected_hits)
+- self.assertTrue(found_result)
++ self.assertTrue(found_result,
++ "Missing all expected hits (%s), instead have: %s"
++ % (", ".join(expected_hits),
++ ", ".join(a.hit_id for a in record.alignments)))
+
+ # Check the expected result(s) are found in the descriptions
+ if expected_hits is None:
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest
new file mode 100644
index 000000000000..9c1f1499ea6f
--- /dev/null
+++ b/sci-biology/bioruby/Manifest
@@ -0,0 +1 @@
+DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7
diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild
new file mode 100644
index 000000000000..b50f3fa137fb
--- /dev/null
+++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+USE_RUBY="ruby19 ruby20"
+
+inherit ruby-fakegem
+
+DESCRIPTION="An integrated environment for bioinformatics using the Ruby language"
+LICENSE="Ruby"
+HOMEPAGE="http://www.bioruby.org/"
+SRC_URI="http://www.${PN}.org/archive/${P}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 ~ppc x86"
+
+ruby_add_rdepend "dev-ruby/libxml"
+
+PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch )
+
+each_ruby_configure() {
+ ${RUBY} setup.rb config || die
+}
+
+each_ruby_compile() {
+ ${RUBY} setup.rb setup || die
+}
+
+each_ruby_install() {
+ ${RUBY} setup.rb install --prefix="${D}" || die
+}
+
+each_ruby_test() {
+ ${RUBY} -rubygems test/runner.rb || die
+}
diff --git a/sci-biology/bioruby/bioruby-9999.ebuild b/sci-biology/bioruby/bioruby-9999.ebuild
new file mode 100644
index 000000000000..838f8430c972
--- /dev/null
+++ b/sci-biology/bioruby/bioruby-9999.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+USE_RUBY="ruby19 ruby20"
+EGIT_REPO_URI="git://github.com/bioruby/bioruby.git
+ https://github.com/bioruby/bioruby.git"
+
+inherit git-2 ruby-fakegem
+
+DESCRIPTION="An integrated environment for bioinformatics using the Ruby language"
+LICENSE="Ruby"
+HOMEPAGE="http://www.bioruby.org/"
+SRC_URI=""
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+ruby_add_rdepend "dev-ruby/libxml"
+
+all_ruby_unpack() {
+ git-2_src_unpack
+}
+
+each_ruby_configure() {
+ ${RUBY} setup.rb config || die
+}
+
+each_ruby_compile() {
+ ${RUBY} setup.rb setup || die
+}
+
+each_ruby_install() {
+ ${RUBY} setup.rb install --prefix="${D}" || die
+}
+
+each_ruby_test() {
+ ${RUBY} -rubygems test/runner.rb || die
+}
diff --git a/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch
new file mode 100644
index 000000000000..71c4ca27104a
--- /dev/null
+++ b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch
@@ -0,0 +1,29 @@
+From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001
+From: Naohisa Goto <ng@bioruby.org>
+Date: Fri, 23 Aug 2013 23:51:59 +0900
+Subject: [PATCH] Test bug fix: Read test file with binary mode to avoid
+ encoding error
+
+ * Test bug fix: Read test file with binary mode to avoid string encoding
+ error. Thanks to nieder (github.com/nieder) who reports the bug.
+ (https://github.com/bioruby/bioruby/issues/84)
+---
+ test/unit/bio/db/test_phyloxml.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/test/unit/bio/db/test_phyloxml.rb b/test/unit/bio/db/test_phyloxml.rb
+index 0744c64..c24278d 100644
+--- a/test/unit/bio/db/test_phyloxml.rb
++++ b/test/unit/bio/db/test_phyloxml.rb
+@@ -100,7 +100,7 @@ def test_open_with_block
+ end
+
+ def test_new
+- str = File.read(TestPhyloXMLData.example_xml)
++ str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read }
+ assert_instance_of(Bio::PhyloXML::Parser,
+ phyloxml = Bio::PhyloXML::Parser.new(str))
+ common_test_next_tree(phyloxml)
+--
+1.8.4
+
diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml
new file mode 100644
index 000000000000..d4648212cbad
--- /dev/null
+++ b/sci-biology/bioruby/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/biosql/Manifest b/sci-biology/biosql/Manifest
new file mode 100644
index 000000000000..cd5198309e65
--- /dev/null
+++ b/sci-biology/biosql/Manifest
@@ -0,0 +1 @@
+DIST biosql-1.0.1.tar.bz2 253516 SHA256 3604ceaf6f3e42a11613b49577b7c68f04d9e094cca4e5d932359c815fc9ad01
diff --git a/sci-biology/biosql/biosql-1.0.1.ebuild b/sci-biology/biosql/biosql-1.0.1.ebuild
new file mode 100644
index 000000000000..ed77d3770701
--- /dev/null
+++ b/sci-biology/biosql/biosql-1.0.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A generic bioinformatics relational database model"
+HOMEPAGE="http://www.biosql.org/"
+SRC_URI="http://biosql.org/DIST/${P}.tar.bz2"
+
+LICENSE="LGPL-3"
+SLOT="0"
+IUSE="mysql postgres"
+KEYWORDS="amd64 x86"
+
+# WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL)
+
+DEPEND="mysql? ( dev-perl/DBD-mysql )
+ postgres? ( dev-perl/DBD-Pg )"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ insinto /usr/share/${PN}
+ doins -r sql scripts/* || die
+ insinto /usr/share/doc/${P}
+ doins -r doc/*
+ dodoc Changes INSTALL README Release.txt
+}
+
+pkg_postinst() {
+ echo
+ elog "Please read the BioSQL schema installation instructions in"
+ elog "/usr/share/doc/${P} to begin using the schema."
+ echo
+}
diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/biosql/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
new file mode 100644
index 000000000000..c1b249e1a095
--- /dev/null
+++ b/sci-biology/blat/Manifest
@@ -0,0 +1 @@
+DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild
new file mode 100644
index 000000000000..c61327420f26
--- /dev/null
+++ b/sci-biology/blat/blat-34-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_PN="${PN}Src"
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
+
+SLOT="0"
+LICENSE="blat"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+IUSE=""
+
+S="${WORKDIR}/${MY_PN}"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+ sed \
+ -e "1i\CFLAGS=${CFLAGS}" \
+ -e "1i\LDFLAGS=${LDFLAGS}" \
+ -i inc/common.mk || die
+ tc-export CC
+}
+
+src_compile() {
+ MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+ mkdir -p "${S}/bin/${MACHTYPE}"
+ emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+ dobin "${S}/bin/${MACHTYPE}/"*
+}
diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild
new file mode 100644
index 000000000000..41d48bf26bd3
--- /dev/null
+++ b/sci-biology/blat/blat-34.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit toolchain-funcs
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+LICENSE="blat"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+MY_PN="${PN}Src"
+SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
+S="${WORKDIR}/${MY_PN}"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+ MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+ sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk"
+ sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk}
+ mkdir -p "${S}/bin/${MACHTYPE}"
+ emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed"
+}
+
+src_install() {
+ MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+ dobin "${S}/bin/${MACHTYPE}/"*
+}
diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch
new file mode 100644
index 000000000000..8bdd05bff68d
--- /dev/null
+++ b/sci-biology/blat/files/34-gentoo.patch
@@ -0,0 +1,226 @@
+ blat/makefile | 2 +-
+ gfClient/makefile | 2 +-
+ gfServer/makefile | 2 +-
+ hg/pslPretty/makefile | 2 +-
+ hg/pslReps/makefile | 2 +-
+ hg/pslSort/makefile | 2 +-
+ inc/common.mk | 11 +++--------
+ makefile | 28 ++++++++++++++--------------
+ utils/faToNib/makefile | 2 +-
+ utils/faToTwoBit/makefile | 2 +-
+ utils/nibFrag/makefile | 2 +-
+ utils/twoBitInfo/makefile | 2 +-
+ utils/twoBitToFa/makefile | 2 +-
+ 13 files changed, 28 insertions(+), 33 deletions(-)
+
+diff --git a/blat/makefile b/blat/makefile
+index b889c7b..739503a 100644
+--- a/blat/makefile
++++ b/blat/makefile
+@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a
+ O = blat.o
+
+ blat: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/blat${EXE}
+
+ all:
+diff --git a/gfClient/makefile b/gfClient/makefile
+index c3288de..36e957e 100644
+--- a/gfClient/makefile
++++ b/gfClient/makefile
+@@ -8,5 +8,5 @@ O = gfClient.o
+ X = gfClient
+
+ gfClient: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/$X${EXE}
+diff --git a/gfServer/makefile b/gfServer/makefile
+index c06b3a5..f042d22 100644
+--- a/gfServer/makefile
++++ b/gfServer/makefile
+@@ -8,7 +8,7 @@ O = gfServer.o
+ X = gfServer
+
+ gfServer: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/$X${EXE}
+
+ test:
+diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile
+index c780b96..cbbcd0d 100644
+--- a/hg/pslPretty/makefile
++++ b/hg/pslPretty/makefile
+@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a
+ O = pslPretty.o
+
+ pslPretty: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
+
+ test:: testRna testDnax
+
+diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile
+index 6e8f6d7..2b73b60 100644
+--- a/hg/pslReps/makefile
++++ b/hg/pslReps/makefile
+@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a
+ O = pslReps.o
+
+ pslReps: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
+
+ lib:
+ cd ../../lib && ${MAKE}
+diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile
+index 81fe083..eb63257 100644
+--- a/hg/pslSort/makefile
++++ b/hg/pslSort/makefile
+@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a
+ O = pslSort.o
+
+ pslSort: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
+
+
+ lib:
+diff --git a/inc/common.mk b/inc/common.mk
+index 1823163..3a04e2b 100644
+--- a/inc/common.mk
++++ b/inc/common.mk
+@@ -1,20 +1,15 @@
+-CC=gcc
+-ifeq (${COPT},)
+- COPT=-O
+-endif
+-CFLAGS=
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+ HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type
+ HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
+
+ # Stronger warning checks, and warnings-->errors, for libraries and CGIs:
+ ifeq (darwin,$(findstring darwin,${OSTYPE}))
+- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable
++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable
+ else
+ ifeq (solaris,$(findstring solaris,${OSTYPE}))
+ HG_WARN_ERR = -DJK_WARN -Wall
+ else
+- HG_WARN_ERR = -DJK_WARN -Wall -Werror
++ HG_WARN_ERR = -DJK_WARN -Wall
+ endif
+ endif
+ # Apply the stronger checks to all code on our development machine:
+@@ -37,7 +32,7 @@ ifeq (${BINDIR},)
+ endif
+ MKDIR=mkdir -p
+ ifeq (${STRIP},)
+- STRIP=strip
++ STRIP=true
+ endif
+ CVS=cvs
+
+diff --git a/makefile b/makefile
+index 6f9fddf..dded1cd 100644
+--- a/makefile
++++ b/makefile
+@@ -1,18 +1,18 @@
+ all:
+- cd lib && ${MAKE}
+- cd jkOwnLib && ${MAKE}
+- cd blat && $(MAKE)
+- cd gfClient && $(MAKE)
+- cd gfServer && $(MAKE)
+- cd hg/pslPretty && $(MAKE)
+- cd hg/pslReps && $(MAKE)
+- cd hg/pslSort && $(MAKE)
+- cd utils/nibFrag && $(MAKE)
+- cd utils/faToNib && $(MAKE)
+- cd utils/faToTwoBit && $(MAKE)
+- cd utils/twoBitToFa && $(MAKE)
+- cd utils/twoBitInfo && $(MAKE)
+- cd webBlat && $(MAKE)
++ $(MAKE) -C lib
++ $(MAKE) -C jkOwnLib
++ $(MAKE) -C blat
++ $(MAKE) -C gfClient
++ $(MAKE) -C gfServer
++ $(MAKE) -C hg/pslPretty
++ $(MAKE) -C hg/pslReps
++ $(MAKE) -C hg/pslSort
++ $(MAKE) -C utils/nibFrag
++ $(MAKE) -C utils/faToNib
++ $(MAKE) -C utils/faToTwoBit
++ $(MAKE) -C utils/twoBitToFa
++ $(MAKE) -C utils/twoBitInfo
++ $(MAKE) -C webBlat
+
+ clean:
+ rm -f */*.o */*/*.o
+diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile
+index fd0e3eb..63a1593 100644
+--- a/utils/faToNib/makefile
++++ b/utils/faToNib/makefile
+@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a
+ O = faToNib.o
+
+ faToNib: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
+diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile
+index b1b44a9..1e8c1c8 100644
+--- a/utils/faToTwoBit/makefile
++++ b/utils/faToTwoBit/makefile
+@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a
+ O = faToTwoBit.o
+
+ faToTwoBit: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
+ ${STRIP} ${BINDIR}/faToTwoBit${EXE}
+
+ clean:
+diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile
+index 260a6f3..e37b9ab 100755
+--- a/utils/nibFrag/makefile
++++ b/utils/nibFrag/makefile
+@@ -4,7 +4,7 @@ include ../../inc/common.mk
+ O = nibFrag.o
+
+ nibFrag: $(O)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
+
+
+
+diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile
+index 649784f..9434d1c 100644
+--- a/utils/twoBitInfo/makefile
++++ b/utils/twoBitInfo/makefile
+@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a
+ O = twoBitInfo.o
+
+ twoBitInfo: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
+ ${STRIP} ${BINDIR}/twoBitInfo${EXE}
+
+ clean:
+diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile
+index cf979f2..081f3b8 100644
+--- a/utils/twoBitToFa/makefile
++++ b/utils/twoBitToFa/makefile
+@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a
+ O = twoBitToFa.o
+
+ twoBitToFa: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
+ #${STRIP} ${BINDIR}/twoBitToFa${EXE}
+
+ clean:
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/blat/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
new file mode 100644
index 000000000000..96859ca6bf5f
--- /dev/null
+++ b/sci-biology/blossoc/Manifest
@@ -0,0 +1 @@
+DIST blossoc-1.4.0.tar.gz 194885 SHA256 b23f51349f72f31263b8aca162c7590a5f52b72fd5e0d91b4a2591098ff5bdbe
diff --git a/sci-biology/blossoc/blossoc-1.4.0.ebuild b/sci-biology/blossoc/blossoc-1.4.0.ebuild
new file mode 100644
index 000000000000..7e5b6694d395
--- /dev/null
+++ b/sci-biology/blossoc/blossoc-1.4.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit autotools eutils
+
+DESCRIPTION="A linkage disequilibrium association mapping tool"
+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/"
+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="sci-libs/gsl
+ dev-libs/boost
+ sci-biology/snpfile"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ sed -i '/TESTS += first_test.sh/ d' "${S}/Makefile.am" || die
+ epatch "${FILESDIR}"/${P}-gcc43.patch
+ eautoreconf
+}
+
+src_install() {
+ emake install DESTDIR="${D}" || die "emake install failed"
+}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
new file mode 100644
index 000000000000..d8e354c1745f
--- /dev/null
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
@@ -0,0 +1,15 @@
+Fixes build with >=GCC-4.3
+
+http://bugs.gentoo.org/show_bug.cgi?id=292949
+
+Patch written by Sebastian Luther <SebastianLuther@gmx.de>
+--- pph.cc
++++ pph.cc
+@@ -23,6 +23,7 @@
+ */
+
+ #include "pph.hh"
++#include <cstdio>
+ #include <cmath>
+ #include <snpfile/matrix.hh>
+ using namespace BiRC::SNPFile;
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/blossoc/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
new file mode 100644
index 000000000000..1345a9e07e4e
--- /dev/null
+++ b/sci-biology/bowtie/Manifest
@@ -0,0 +1,2 @@
+DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
+DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000000000000..c26c986ed194
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS=""
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL
+}
diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild
new file mode 100644
index 000000000000..b8181190243c
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.0.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL doc/README
+ dohtml doc/{manual.html,style.css}
+}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
new file mode 100644
index 000000000000..3c8a1e1d9ca4
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
@@ -0,0 +1,45 @@
+ alphabet.h | 24 ++++++++++++------------
+ 1 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/alphabet.h b/alphabet.h
+index b464ddf..08d0281 100644
+--- a/alphabet.h
++++ b/alphabet.h
+@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
+ return s_rc;
+ }
+
++/// Reverse a string in-place
++template <typename TStr>
++static inline void reverseInPlace(TStr& s) {
++ typedef typename Value<TStr>::Type TVal;
++ size_t len = length(s);
++ for(size_t i = 0; i < (len>>1); i++) {
++ TVal tmp = s[i];
++ s[i] = s[len-i-1];
++ s[len-i-1] = tmp;
++ }
++}
++
+ /**
+ * Reverse-complement s in-place. Ns go to Ns.
+ */
+@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ }
+ }
+
+-/// Reverse a string in-place
+-template <typename TStr>
+-static inline void reverseInPlace(TStr& s) {
+- typedef typename Value<TStr>::Type TVal;
+- size_t len = length(s);
+- for(size_t i = 0; i < (len>>1); i++) {
+- TVal tmp = s[i];
+- s[i] = s[len-i-1];
+- s[len-i-1] = tmp;
+- }
+-}
+-
+ /**
+ * Return the reverse-complement of s.
+ */
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
new file mode 100644
index 000000000000..e493417070fb
--- /dev/null
+++ b/sci-biology/bowtie/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">bowtie-bio</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
new file mode 100644
index 000000000000..9c0d995bfb1f
--- /dev/null
+++ b/sci-biology/bwa/Manifest
@@ -0,0 +1 @@
+DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild
new file mode 100644
index 000000000000..76ed0cca912b
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.7.12.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~x64-macos"
+
+PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )
+
+src_prepare() {
+ epatch ${PATCHES[@]}
+ tc-export CC AR
+}
+
+src_install() {
+ dobin bwa
+
+ doman bwa.1
+
+ exeinto /usr/libexec/${PN}
+ doexe qualfa2fq.pl xa2multi.pl
+
+ dodoc NEWS.md README-alt.md README.md
+}
diff --git a/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
new file mode 100644
index 000000000000..406e9b052376
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch
@@ -0,0 +1,27 @@
+--- Makefile
++++ Makefile
+@@ -1,8 +1,8 @@
+-CC= gcc
++CC?= gcc
+ #CC= clang --analyze
+-CFLAGS= -g -Wall -Wno-unused-function -O2
++CFLAGS?= -g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR= ar
++AR?= ar
+ DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -26,10 +26,10 @@
+ all:$(PROG)
+
+ bwa:libbwa.a $(AOBJS) main.o
+- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+ bwamem-lite:libbwa.a example.o
+- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+
+ libbwa.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
new file mode 100644
index 000000000000..97a33fbf5c42
--- /dev/null
+++ b/sci-biology/bwa/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">bio-bwa</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
new file mode 100644
index 000000000000..c3cf3842c604
--- /dev/null
+++ b/sci-biology/cd-hit/Manifest
@@ -0,0 +1,3 @@
+DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281
+DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 RMD160 00fca8d2527a4a6b1eda861f8f750e10ee565ae7 SHA1 743c4b6ec79b9d5acd1e1171587e96c03e3e3003 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a
+DIST cd-hit-v4.6-2012-04-25.tgz 652228 RMD160 318239a9416fd3cd57754546c8fcc0a4cea7f5d8 SHA1 e47c662c0a284ae99e47205d6a4eaea805a76cae SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9
diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
new file mode 100644
index 000000000000..d47948f0d821
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2011-01-31"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+ use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+ tc-export CXX
+ use openmp || append-flags -DNO_OPENMP
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+ local myconf=
+ use openmp && myconf="openmp=yes"
+ emake ${myconf} || die
+}
+
+src_install() {
+ dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die
+ dodoc ChangeLog cdhit-user-guide.pdf || die
+}
diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
new file mode 100644
index 000000000000..bafa3301d724
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2011-03-07"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+ use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+ tc-export CXX
+ use openmp || append-flags -DNO_OPENMP
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+ local myconf=
+ use openmp && myconf="openmp=yes"
+ emake ${myconf}
+}
+
+src_install() {
+ dodir /usr/bin
+ emake PREFIX="${ED}/usr/bin" install
+ dodoc ChangeLog cdhit-user-guide.pdf
+}
diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild
new file mode 100644
index 000000000000..d7dd15559c5c
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-04-25"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+ use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+ tc-export CXX
+ use openmp || append-flags -DNO_OPENMP
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+ local myconf=
+ use openmp && myconf="openmp=yes"
+ emake ${myconf}
+}
+
+src_install() {
+ dodir /usr/bin
+ emake PREFIX="${ED}/usr/bin" install
+ dodoc ChangeLog
+ use doc && dodoc doc/*
+}
diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
new file mode 100644
index 000000000000..c3eaf79cc8f2
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
@@ -0,0 +1,85 @@
+diff --git a/Makefile b/Makefile
+index f1eaa26..92d3130 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
+ # in command line:
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -O2 -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+
+ # support debugging
+@@ -18,16 +18,16 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += -ggdb
+ endif
+
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++LDFLAGS += -o
+
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div
+
+ .c++.o:
+- $(CC) $(CCFLAGS) -c $<
++ $(CXX) $(CXXFLAGS) -c $<
+
+ all: $(PROGS)
+
+@@ -37,39 +37,39 @@ clean:
+ # programs
+
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-common.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-utility.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+
+ cdhit.o: cdhit.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit.c++ -c
+
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-div.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+
diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
new file mode 100644
index 000000000000..5aa9b79e02ae
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
@@ -0,0 +1,98 @@
+ Makefile | 36 ++++++++++++++++++------------------
+ 1 files changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e8bac1d..bd31093 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
+ # in command line:
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -O2 -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+
+ # support debugging
+@@ -18,16 +18,16 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += -ggdb
+ endif
+
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++LDFLAGS += -o
+
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+
+ .c++.o:
+- $(CC) $(CCFLAGS) -c $<
++ $(CXX) $(CXXFLAGS) -c $<
+
+ all: $(PROGS)
+
+@@ -37,47 +37,47 @@ clean:
+ # programs
+
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++ $(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
+
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-common.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-utility.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+
+ cdhit.o: cdhit.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit.c++ -c
+
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-div.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-454.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+
+ PREFIX ?= /usr/local/bin
+
diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
new file mode 100644
index 000000000000..7a376eb8e73c
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.6-gentoo.patch
@@ -0,0 +1,117 @@
+ Makefile | 47 ++++++++++++++++++++++-------------------------
+ 1 files changed, 22 insertions(+), 25 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e9796a1..97dd72b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,16 +1,13 @@
+-
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++
+
+ # without OpenMP
+-CCFLAGS = -DNO_OPENMP
++#CXXFLAGS = -DNO_OPENMP
+
+ # with OpenMP
+ # in command line:
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+
+ # support debugging
+@@ -18,22 +15,22 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS +=
+ else
+-CCFLAGS += -O2
++CXXFLAGS +=
+ endif
+
+ ifdef MAX_SEQ
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+ endif
+
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++#LDFLAGS += -o
+
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+
+ .c++.o:
+- $(CC) $(CCFLAGS) -c $<
++ $(CXX) $(CXXFLAGS) -c $<
+
+ all: $(PROGS)
+
+@@ -43,47 +40,47 @@ clean:
+ # programs
+
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
+
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
+
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
+
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
+
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
+
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
+
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-common.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-utility.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+
+ cdhit.o: cdhit.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit.c++ -c
+
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-div.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+- $(CC) $(CCFLAGS) cdhit-454.c++ -c
++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+
+ PREFIX ?= /usr/local/bin
+
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
new file mode 100644
index 000000000000..bd5607ab16b5
--- /dev/null
+++ b/sci-biology/cd-hit/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+CD-HIT is a very widely used program for clustering and comparing large sets
+of protein or nucleotide sequences. CD-HIT is very fast and can handle
+extremely large databases. CD-HIT helps to significantly reduce the
+computational and manual efforts in many sequence analysis tasks and aids in
+understanding the data structure and correct the bias within a dataset.
+The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D,
+CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT
+(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a
+user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2
+datasets and identifies the sequences in db2 that are similar to db1 above
+a threshold. CD-HIT-454 is a program to identify natural and artificial
+duplicates from pyrosequencing reads. The usage of other programs and
+scripts can be found in CD-HIT user's guide.
+</longdescription>
+ <upstream>
+ <remote-id type="google-code">cdhit</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest
new file mode 100644
index 000000000000..2394b3a452f6
--- /dev/null
+++ b/sci-biology/clustal-omega/Manifest
@@ -0,0 +1,2 @@
+DIST clustal-omega-1.2.0.tar.gz 1156741 SHA256 cbf5ad4e1ce88641cca307be1edfe95d3882997d71c11b43c8e1fcd6e388c61d SHA512 d207699e1158178e2d7122620026b199251ab86bcc3f72a08d58f23e2dd5c2961340e872a13c34f1d6832c5eef5ff8ab09c43f0cb51a81d6c4ef554f936434e2 WHIRLPOOL 41505b42829d440fd312f1538ef78fb7d0f668008cd00bcc52022139eb2ff21d05d89519af2a18e5a2f845e24a5d374a81eb4163c2720a32f71ead7ce40e4eac
+DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256 0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512 1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de WHIRLPOOL b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577
diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild
new file mode 100644
index 000000000000..ccded19116cd
--- /dev/null
+++ b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Scalable multiple alignment of protein sequences"
+HOMEPAGE="http://www.clustal.org/omega/"
+SRC_URI="http://www.clustal.org/omega/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="dev-libs/argtable"
+RDEPEND="${DEPEND}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+ sed \
+ -e "s:-O3::g" \
+ -i configure.ac || die
+ autotools-utils_src_prepare
+}
+
+src_install() {
+ autotools-utils_src_install
+ if ! use static-libs; then
+ rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+ rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die
+ fi
+}
diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild
new file mode 100644
index 000000000000..e56766f9416e
--- /dev/null
+++ b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Scalable multiple alignment of protein sequences"
+HOMEPAGE="http://www.clustal.org/omega/"
+SRC_URI="http://www.clustal.org/omega/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="dev-libs/argtable"
+RDEPEND="${DEPEND}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+ sed \
+ -e "s:-O3::g" \
+ -i configure.ac || die
+ autotools-utils_src_prepare
+}
+
+src_install() {
+ autotools-utils_src_install
+ if ! use static-libs; then
+ rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+ rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die
+ fi
+}
diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/clustal-omega/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
new file mode 100644
index 000000000000..b1f7bb630cd0
--- /dev/null
+++ b/sci-biology/clustalw-mpi/Manifest
@@ -0,0 +1 @@
+DIST clustalw-mpi-0.13.tar.gz 154911 RMD160 9da3e418efcb0cfd0c5df2705ee217b9dacc3917 SHA1 ae5026e8b4ba58bb0caa5643ea90434d9589df5a SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
new file mode 100644
index 000000000000..11f1e57e2731
--- /dev/null
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm"
+HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"
+SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="public-domain"
+IUSE="mpi_njtree static_pairalign"
+
+DEPEND="virtual/mpi"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+ if use mpi_njtree; then
+ sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
+ die "Failed to configure MPI code for NJ trees."
+ fi
+ if use static_pairalign; then
+ sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
+ die "Failed to configure static scheduling for pair alignments."
+ fi
+}
+
+src_install() {
+ dobin ${PN}
+ newdoc README.${PN} README
+}
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
new file mode 100644
index 000000000000..6e36061cbb39
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
@@ -0,0 +1,23 @@
+ Makefile | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index f2107ce..835232b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE
+ PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN
+ #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+
+-CFLAGS = -c -O3
++CFLAGS += -c
+ #CFLAGS = -c -O3 -funroll-all-loops
+-LFLAGS = -lm
++LIBS = -lm
+
+ clustalw-mpi: $(OBJECTS)
+- $(CC) -o $@ $(OBJECTS) $(LFLAGS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+
+ interface.o : interface.c $(HEADERS) param.h
+ $(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
new file mode 100644
index 000000000000..905eba1a07b8
--- /dev/null
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<use>
+ <flag name='mpi_njtree'>Use MPI (as opposed to serial) code for computing
+ neighbor-joining trees</flag>
+ <flag name='static_pairalign'>Use static (as opposed to dynamic) scheduling
+ for pair alignments</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
new file mode 100644
index 000000000000..7d1b7dca8a7f
--- /dev/null
+++ b/sci-biology/clustalw/Manifest
@@ -0,0 +1,2 @@
+DIST clustalw-2.1.tar.gz 350761 SHA256 e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921 WHIRLPOOL 93158f400cbdf11ecddcac15b5b4cee9af61d9b933f7100ad18d01d346de54c6bad5a9a12fe5a70a265c92581d3ee9cfbc41b17ee2c2ff80ff2a6658efba5f40
+DIST clustalw1.83.UNIX.tar.gz 166863 SHA256 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60 SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a WHIRLPOOL 5a075579737d8a9ba5f62d6f90feb53a275bd31a8131d1b7d21395cf46cfefbdf4e48563b55734c995b9e3d8f9c37c78ea77f4e48920d64781190645ea36112b
diff --git a/sci-biology/clustalw/clustalw-1.83-r3.ebuild b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
new file mode 100644
index 000000000000..6047a08ed466
--- /dev/null
+++ b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
+HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
+
+LICENSE="clustalw"
+SLOT="1"
+KEYWORDS="alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE=""
+
+S="${WORKDIR}"/${PN}${PV}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-as-needed.patch
+
+ sed \
+ -e "/^CC/s:cc:$(tc-getCC):g" \
+ -i makefile || die
+ sed \
+ -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \
+ -i clustalw.c || die
+}
+
+src_install() {
+ dobin clustalw
+ dodoc README clustalv.doc clustalw.doc clustalw.ms
+ insinto /usr/share/doc/${PF}
+ doins clustalw_help
+}
diff --git a/sci-biology/clustalw/clustalw-2.1.ebuild b/sci-biology/clustalw/clustalw-2.1.ebuild
new file mode 100644
index 000000000000..8664ee3108ec
--- /dev/null
+++ b/sci-biology/clustalw/clustalw-2.1.ebuild
@@ -0,0 +1,14 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
+HOMEPAGE="http://www.clustal.org/"
+SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="2"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE=""
diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch
new file mode 100644
index 000000000000..62b4654cddea
--- /dev/null
+++ b/sci-biology/clustalw/files/1.83-as-needed.patch
@@ -0,0 +1,17 @@
+--- makefile 2003-01-29 09:53:45.000000000 +0100
++++ makefile.new 2009-08-17 08:33:16.000000000 +0200
+@@ -11,11 +11,11 @@
+ HEADERS = general.h clustalw.h
+
+ CC = cc
+-CFLAGS = -c -O
+-LFLAGS = -O -lm
++CFLAGS += -c
++LIBS = -lm
+
+ clustalw : $(OBJECTS) amenu.o clustalw.o
+- $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
+
+ interface.o : interface.c $(HEADERS) param.h
+ $(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/clustalw/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
new file mode 100644
index 000000000000..acbf2db29963
--- /dev/null
+++ b/sci-biology/clustalx/Manifest
@@ -0,0 +1 @@
+DIST clustalx-2.1.tar.gz 341649 SHA256 e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 WHIRLPOOL 6cbe8dcf2be3a535e8ac0ef0b9b476d4429a80bd94b394c0194f46ed039f9ac2b97b0ec2ed680838a0973b3187b2dbc90285733657975e03288b9840ba3d6b15
diff --git a/sci-biology/clustalx/clustalx-2.1-r1.ebuild b/sci-biology/clustalx/clustalx-2.1-r1.ebuild
new file mode 100644
index 000000000000..9aa885eaa5bb
--- /dev/null
+++ b/sci-biology/clustalx/clustalx-2.1-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils qt4-r2
+
+DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
+HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/"
+SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+DEPEND="
+ dev-qt/qtcore:4
+ dev-qt/qtgui:4"
+RDEPEND="${DEPEND}
+ >=sci-biology/clustalw-${PV}"
+
+src_prepare() {
+ sed \
+ -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \
+ -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \
+ -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \
+ -i ClustalQtParams.h || \
+ die "Failed to patch shared files location."
+ sed \
+ -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \
+ -i HelpDisplayWidget.cpp || \
+ die "Failed to patch help file location."
+ rm -rf usr || die
+}
+
+src_install() {
+ dobin clustalx
+ insinto /usr/share/${PN}
+ doins colprot.xml coldna.xml colprint.xml clustalx.hlp
+ make_desktop_entry ${PN} ClustalX
+}
diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/clustalx/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
new file mode 100644
index 000000000000..e9cd6b128266
--- /dev/null
+++ b/sci-biology/consed/Manifest
@@ -0,0 +1,4 @@
+DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089
+DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3
+DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
+DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21
diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild
new file mode 100644
index 000000000000..3ce704e8792f
--- /dev/null
+++ b/sci-biology/consed/consed-19-r2.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+ ${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+ >=sci-biology/phred-000925
+ >=sci-biology/phrap-1.080721"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please visit ${HOMEPAGE} and obtain the file"
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
+ einfo "and place it in ${DISTDIR},"
+ einfo "obtain the file"
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
+ einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+ sed -i \
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+ sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
+}
+
+src_compile() {
+ emake || die
+ emake -C misc/mktrace || die
+ emake -C misc/phd2fasta || die
+ (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
+ dobin scripts/* contributions/* || die
+ insinto /usr/lib/screenLibs
+ doins misc/*.{fa*,seq} || die
+ insinto /usr/share/${PN}/examples
+ doins -r standard polyphred autofinish assembly_view 454_newbler \
+ align454reads align454reads_answer solexa_example \
+ solexa_example_answer selectRegions selectRegionsAnswer || die
+ echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+ doenvd "${S}/99consed" || die
+ dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+ einfo "Package documentation is available at"
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}
diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
new file mode 100644
index 000000000000..0bf33a7278cf
--- /dev/null
+++ b/sci-biology/consed/consed-27.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="
+ ${P}-sources.tar.gz
+ ${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+ sci-biology/samtools
+ >=sci-biology/phred-000925
+ >=sci-biology/phrap-1.080721
+ dev-lang/perl"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please visit ${HOMEPAGE} and obtain the file"
+ einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
+ einfo "and place it in ${DISTDIR},"
+ einfo "obtain the file"
+ einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
+ einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+ sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+ sed -i \
+ -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
+ -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+ -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+ -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
+ sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+ sed \
+ -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+ -i "${S}"/scripts/* || die
+}
+
+src_compile() {
+ emake
+ emake -C misc/mktrace
+ emake -C misc/phd2fasta
+ (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+ dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
+ dobin scripts/* contributions/*
+ insinto /usr/lib/screenLibs
+ doins misc/*.{fa*,seq}
+ insinto /usr/share/${PN}/examples
+ doins -r \
+ standard polyphred autofinish assembly_view 454_newbler \
+ align454reads align454reads_answer solexa_example \
+ solexa_example_answer selectRegions selectRegionsAnswer
+ echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
+ echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
+ mkdir -p "${ED}"/etc/consedrc || die
+ touch "${ED}"/etc/consedrc || die
+ doenvd "${S}/99consed" || die
+ sed \
+ -e "s#/usr/local/genome#${EPREFIX}/usr#" \
+ -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
+ sed \
+ -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
+ -i "${ED}"/usr/bin/phredPhrap || die
+ sed \
+ -e 's#/wt1/gordon/genome#/usr/bin#' \
+ -i "${ED}"/usr/bin/fastq2Phrap.perl || die
+ dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+ einfo "Package documentation is available at"
+ einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}
diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/consed/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
new file mode 100644
index 000000000000..017836ee07ad
--- /dev/null
+++ b/sci-biology/cufflinks/Manifest
@@ -0,0 +1,2 @@
+DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce
+DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224
diff --git a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
new file mode 100644
index 000000000000..36322f463de6
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ >=sci-biology/samtools-0.1.18
+ <sci-biology/samtools-1
+ <dev-libs/boost-1.56:="
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-autotools.patch
+ "${FILESDIR}"/${P}-boost.patch
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ )
+
+src_configure() {
+ local myeconfargs=(
+ --disable-optim
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
+ --with-bam="${EPREFIX}/usr/"
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
new file mode 100644
index 000000000000..66298cbc1972
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ || (
+ (
+ >=sci-biology/samtools-0.1.18
+ sci-libs/htslib
+ )
+ <sci-biology/samtools-1
+ )
+ >=dev-libs/boost-1.47.0:=
+ <dev-libs/boost-1.56.0:=
+ dev-cpp/eigen:3
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-hts.patch
+ "${FILESDIR}"/${P}-flags.patch
+ )
+
+src_prepare() {
+ append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --disable-optim
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
+ --with-bam="${EPREFIX}/usr/"
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild
new file mode 100644
index 000000000000..5e7f763389f9
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ >=sci-biology/samtools-0.1.18
+ <sci-biology/samtools-1
+ >=dev-libs/boost-1.47.0:=
+ <dev-libs/boost-1.56.0:=
+ dev-cpp/eigen:3
+"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --disable-optim
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
+ --with-bam="${EPREFIX}/usr/"
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
new file mode 100644
index 000000000000..73e52b4343a0
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
@@ -0,0 +1,38 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -27,6 +27,7 @@ AC_PROG_AWK
+ AC_PROG_CXX
+ AC_PROG_CC
+ AC_PROG_MAKE_SET
++AM_PROG_AR
+ AC_PROG_RANLIB
+ AC_PROG_INSTALL
+ AM_PATH_PYTHON([2.4])
+@@ -54,7 +55,7 @@ AC_CANONICAL_HOST
+
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ #echo "${host_cpu}-${host_os}"
+@@ -99,15 +100,15 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with
+ [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
+
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
+-CXXFLAGS="$CFLAGS"
++CXXFLAGS="$CXXFLAGS"
+ CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
+-LDFLAGS="$ext_LDFLAGS"
++LDFLAGS="$LDFLAGS $ext_LDFLAGS"
+
+ # Checks for structures/functions that can be used to determine system memory
+ AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>])
+ AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>])
+
+-AM_INIT_AUTOMAKE([-Wall -Werror tar-pax foreign])
++AM_INIT_AUTOMAKE([-Wall tar-pax foreign subdir-objects])
+
+ AC_CONFIG_FILES([Makefile
+ src/Makefile])
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch
new file mode 100644
index 000000000000..d45391bf4f3a
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch
@@ -0,0 +1,1320 @@
+ ax_boost_thread.m4 | 6 +++---
+ src/abundances.cpp | 56 +++++++++++++++++++++++++-------------------------
+ src/biascorrection.cpp | 2 +-
+ src/bundles.cpp | 10 ++++-----
+ src/bundles.h | 10 ++++-----
+ src/common.h | 4 ++--
+ src/compress_gtf.cpp | 12 +++++------
+ src/cuffdiff.cpp | 30 +++++++++++++--------------
+ src/cufflinks.cpp | 34 +++++++++++++++---------------
+ src/differential.cpp | 38 +++++++++++++++++-----------------
+ src/filters.cpp | 8 ++++----
+ src/genes.h | 6 +++---
+ src/gtf_to_sam.cpp | 8 ++++----
+ src/hits.cpp | 4 ++--
+ src/replicates.cpp | 6 +++---
+ src/replicates.h | 18 ++++++++--------
+ src/scaffolds.cpp | 28 ++++++++++++-------------
+ src/scaffolds.h | 2 +-
+ 18 files changed, 141 insertions(+), 141 deletions(-)
+
+diff --git a/ax_boost_thread.m4 b/ax_boost_thread.m4
+index d1d42f6..6f99f1b 100644
+--- a/ax_boost_thread.m4
++++ b/ax_boost_thread.m4
+@@ -105,20 +105,20 @@ AC_DEFUN([AX_BOOST_THREAD],
+ for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
+ [link_thread="no"])
+ done
+ if test "x$link_thread" != "xyes"; then
+ for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
+ [link_thread="no"])
+ done
+ fi
+
+ else
+- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
++ BOOST_THREAD_LIB="$ax_boost_user_thread_lib -lboost_system";
+ AC_SUBST(BOOST_THREAD_LIB)
+ link_thread="yes";
+
+diff --git a/src/abundances.cpp b/src/abundances.cpp
+index d8f81d0..6e717dc 100644
+--- a/src/abundances.cpp
++++ b/src/abundances.cpp
+@@ -140,7 +140,7 @@ AbundanceStatus AbundanceGroup::status() const
+ {
+ bool has_lowdata_member = false;
+ bool has_ok_member = false;
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ if (ab->status() == NUMERIC_FAIL)
+ {
+@@ -205,7 +205,7 @@ void TranscriptAbundance::FPKM_variance(double v)
+
+ bool AbundanceGroup::has_member_with_status(AbundanceStatus member_status)
+ {
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ if (ab->status() == member_status)
+ {
+@@ -219,7 +219,7 @@ double AbundanceGroup::num_fragments() const
+ {
+ double num_f = 0;
+
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ num_f += ab->num_fragments();
+ }
+@@ -231,7 +231,7 @@ double AbundanceGroup::mass_fraction() const
+ {
+ double mass = 0;
+
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ mass += ab->mass_fraction();
+ }
+@@ -242,7 +242,7 @@ double AbundanceGroup::mass_variance() const
+ {
+ double mass_var = 0;
+
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ mass_var += ab->mass_variance();
+ }
+@@ -253,7 +253,7 @@ double AbundanceGroup::FPKM() const
+ {
+ double fpkm = 0;
+
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ fpkm += ab->FPKM();
+ }
+@@ -265,7 +265,7 @@ double AbundanceGroup::gamma() const
+ {
+ double gamma = 0;
+
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ gamma += ab->gamma();
+ }
+@@ -281,7 +281,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep,
+ assert (to_keep.size() == _abundances.size());
+
+ size_t num_kept = 0;
+- foreach(bool keeper, to_keep)
++ for_each(bool keeper, to_keep)
+ {
+ num_kept += keeper;
+ }
+@@ -331,7 +331,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep,
+ void AbundanceGroup::get_transfrags(vector<shared_ptr<Abundance> >& transfrags) const
+ {
+ transfrags.clear();
+- foreach(shared_ptr<Abundance> pA, _abundances)
++ for_each(shared_ptr<Abundance> pA, _abundances)
+ {
+ shared_ptr<Scaffold> pS = pA->transfrag();
+ if (pS)
+@@ -345,7 +345,7 @@ set<string> AbundanceGroup::gene_id() const
+ {
+ set<string> s;
+
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ set<string> sub = pA->gene_id();
+ s.insert(sub.begin(), sub.end());
+@@ -358,7 +358,7 @@ set<string> AbundanceGroup::gene_name() const
+ {
+ set<string> s;
+
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ set<string> sub = pA->gene_name();
+ s.insert(sub.begin(), sub.end());
+@@ -372,7 +372,7 @@ set<string> AbundanceGroup::tss_id() const
+ {
+ set<string> s;
+
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ set<string> sub = pA->tss_id();
+ s.insert(sub.begin(), sub.end());
+@@ -385,7 +385,7 @@ set<string> AbundanceGroup::protein_id() const
+ {
+ set<string> s;
+
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ set<string> sub = pA->protein_id();
+ s.insert(sub.begin(), sub.end());
+@@ -398,7 +398,7 @@ const string& AbundanceGroup::locus_tag() const
+ {
+ static string default_locus_tag = "-";
+ const string* pLast = NULL;
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ if (pLast)
+ {
+@@ -422,7 +422,7 @@ const string& AbundanceGroup::reference_tag() const
+ {
+ static string default_reference_tag = "-";
+ const string* pLast = NULL;
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ if (pLast)
+ {
+@@ -448,7 +448,7 @@ double AbundanceGroup::effective_length() const
+ double group_fpkm = FPKM();
+ if (group_fpkm == 0)
+ return 0;
+- foreach (shared_ptr<Abundance> ab, _abundances)
++ for_each (shared_ptr<Abundance> ab, _abundances)
+ {
+ eff_len += (ab->effective_length() * (ab->FPKM() / group_fpkm));
+ }
+@@ -1216,7 +1216,7 @@ void AbundanceGroup::estimate_count_covariance()
+ {
+ // if the entire group is unstable, then set LOWDATA on all members of
+ // it to reduce false positives in differential expression analysis.
+- foreach(shared_ptr<Abundance> ab, _abundances)
++ for_each(shared_ptr<Abundance> ab, _abundances)
+ {
+ ab->status(NUMERIC_LOW_DATA);
+ }
+@@ -1468,7 +1468,7 @@ void AbundanceGroup::calculate_conf_intervals()
+ double sum_transfrag_FPKM_hi = 0;
+ double max_fpkm = 0.0;
+ //double min_fpkm = 1e100;
+- foreach(shared_ptr<Abundance> pA, _abundances)
++ for_each(shared_ptr<Abundance> pA, _abundances)
+ {
+ double FPKM_hi;
+ double FPKM_lo;
+@@ -1586,7 +1586,7 @@ void AbundanceGroup::calculate_conf_intervals()
+ // double sum_transfrag_FPKM_hi = 0;
+ // double max_fpkm = 0.0;
+ // //double min_fpkm = 1e100;
+-// foreach(shared_ptr<Abundance> pA, _abundances)
++// for_each(shared_ptr<Abundance> pA, _abundances)
+ // {
+ // double FPKM_hi;
+ // double FPKM_lo;
+@@ -1732,7 +1732,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments,
+ if (mapped_transcripts.empty())
+ {
+ //gammas = vector<double>(transfrags.size(), 0.0);
+- foreach (shared_ptr<Abundance> ab, _abundances)
++ for_each (shared_ptr<Abundance> ab, _abundances)
+ {
+ ab->gamma(0);
+ }
+@@ -1783,7 +1783,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments,
+ if (filtered_transcripts.empty())
+ {
+ //gammas = vector<double>(transfrags.size(), 0.0);
+- foreach (shared_ptr<Abundance> ab, _abundances)
++ for_each (shared_ptr<Abundance> ab, _abundances)
+ {
+ ab->gamma(0);
+ }
+@@ -2117,7 +2117,7 @@ void AbundanceGroup::calculate_kappas()
+ double S_FPKM = 0.0;
+ double Z_kappa = 0.0;
+ double X_S = 0.0;
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ if (pA->effective_length() > 0)
+ {
+@@ -2128,7 +2128,7 @@ void AbundanceGroup::calculate_kappas()
+ }
+
+ //fprintf (stderr, "*********\n");
+- foreach (shared_ptr<Abundance> pA, _abundances)
++ for_each (shared_ptr<Abundance> pA, _abundances)
+ {
+ if (S_FPKM > 0)
+ {
+@@ -2201,7 +2201,7 @@ void get_alignments_from_scaffolds(const vector<shared_ptr<Abundance> >& abundan
+ {
+ set<const MateHit*> hits_in_gene_set;
+
+- foreach(shared_ptr<Abundance> pA, abundances)
++ for_each(shared_ptr<Abundance> pA, abundances)
+ {
+ shared_ptr<Scaffold> pS = pA->transfrag();
+ assert (pS);
+@@ -2787,7 +2787,7 @@ AbundanceStatus empirical_mean_replicate_gamma_mle(const vector<shared_ptr<Abund
+ gamma_covariance = ublas::zero_matrix<double>(N,N);
+ ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N);
+ //
+- foreach(ublas::vector<double>& mle, mle_gammas)
++ for_each(ublas::vector<double>& mle, mle_gammas)
+ {
+ expected_mle_gamma += mle;
+ }
+@@ -3122,7 +3122,7 @@ AbundanceStatus bootstrap_gamma_mle(const vector<shared_ptr<Abundance> >& transc
+ gamma_covariance = ublas::zero_matrix<double>(N,N);
+ ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N);
+
+- foreach(ublas::vector<double>& mle, mle_gammas)
++ for_each(ublas::vector<double>& mle, mle_gammas)
+ {
+ //cerr << "MLE # "<< MLENUM++ << endl;
+ //cerr << mle << endl;
+@@ -3586,7 +3586,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts,
+
+ double round_err = 0.0;
+ double num_good = 0;
+- foreach (double& g, gammas)
++ for_each (double& g, gammas)
+ {
+ if (g < min_isoform_fraction)
+ {
+@@ -3598,7 +3598,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts,
+ num_good += 1;
+ }
+ }
+- foreach (double& g, gammas)
++ for_each (double& g, gammas)
+ {
+ if (g != 0)
+ {
+diff --git a/src/biascorrection.cpp b/src/biascorrection.cpp
+index 0d49851..55884f4 100644
+--- a/src/biascorrection.cpp
++++ b/src/biascorrection.cpp
+@@ -207,7 +207,7 @@ void BiasLearner::preProcessTranscript(const Scaffold& transcript)
+ vector<double> startHist(transcript.length()+1, 0.0); // +1 catches overhangs
+ vector<double> endHist(transcript.length()+1, 0.0);
+
+- foreach (const MateHit* hit_p, transcript.mate_hits())
++ for_each (const MateHit* hit_p, transcript.mate_hits())
+ {
+ const MateHit& hit = *hit_p;
+ if (!hit.left_alignment() && !hit.right_alignment())
+diff --git a/src/bundles.cpp b/src/bundles.cpp
+index ead07f2..a392514 100644
+--- a/src/bundles.cpp
++++ b/src/bundles.cpp
+@@ -228,7 +228,7 @@ void load_ref_rnas(FILE* ref_mRNA_file,
+ }
+ }
+
+- foreach (shared_ptr<Scaffold> s, ref_mRNAs)
++ for_each (shared_ptr<Scaffold> s, ref_mRNAs)
+ {
+ assert (s);
+ }
+@@ -418,7 +418,7 @@ void HitBundle::finalize_open_mates()
+
+ for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr)
+ {
+- foreach (MateHit& hit, itr->second)
++ for_each (MateHit& hit, itr->second)
+ {
+ delete hit.left_alignment();
+ delete hit.right_alignment();
+@@ -438,7 +438,7 @@ void HitBundle::remove_hitless_scaffolds()
+ void HitBundle::remove_unmapped_hits()
+ {
+
+- foreach (MateHit& hit, _hits)
++ for_each (MateHit& hit, _hits)
+ {
+ if (unmapped_hit(hit))
+ {
+@@ -586,7 +586,7 @@ void HitBundle::finalize(bool is_combined)
+ }
+ else
+ {
+- foreach (MateHit& hit, _hits)
++ for_each (MateHit& hit, _hits)
+ {
+ hit.incr_collapse_mass(hit.common_scale_mass());
+ }
+@@ -1316,7 +1316,7 @@ void identify_bad_splices(const HitBundle& bundle,
+ ins_itr = bad_splice_ops.insert(make_pair(ref_id, vector<AugmentedCuffOp>()));
+ vector<AugmentedCuffOp>& bad_introns = ins_itr.first->second;
+
+- foreach (const MateHit& hit, bundle.hits())
++ for_each (const MateHit& hit, bundle.hits())
+ {
+ if (hit.left_alignment())
+ {
+diff --git a/src/bundles.h b/src/bundles.h
+index 15f51ee..aec725e 100644
+--- a/src/bundles.h
++++ b/src/bundles.h
+@@ -57,7 +57,7 @@ public:
+ ~HitBundle()
+ {
+ vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds();
+- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
+ {
+ // This bundle and the factory that actually owns the ref_mRNAs
+ // are the only objects that should have access to these scaffolds
+@@ -73,7 +73,7 @@ public:
+ }
+ }
+
+- foreach (MateHit& hit, _hits)
++ for_each (MateHit& hit, _hits)
+ {
+ delete hit.left_alignment();
+ delete hit.right_alignment();
+@@ -81,7 +81,7 @@ public:
+
+ for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr)
+ {
+- foreach (MateHit& hit, itr->second)
++ for_each (MateHit& hit, itr->second)
+ {
+ delete hit.left_alignment();
+ delete hit.right_alignment();
+@@ -113,7 +113,7 @@ public:
+ _hits.clear();
+ _non_redundant.clear();
+ vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds();
+- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
+ {
+ if (ref_scaff.use_count() <= 3)
+ {
+@@ -250,7 +250,7 @@ public:
+ next_ref_scaff = ref_mRNAs.begin();
+ next_mask_scaff = mask_gtf_recs.begin();
+
+- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
+ {
+ ref_scaff->clear_hits();
+ }
+diff --git a/src/common.h b/src/common.h
+index b715e9c..1ed7d77 100644
+--- a/src/common.h
++++ b/src/common.h
+@@ -22,8 +22,8 @@
+ using boost::math::normal;
+
+ #include <boost/foreach.hpp>
+-#define foreach BOOST_FOREACH
+-#define reverse_foreach BOOST_REVERSE_FOREACH
++#define for_each BOOST_FOREACH
++#define reverse_for_each BOOST_REVERSE_FOREACH
+
+ #include <boost/thread.hpp>
+ #include <boost/shared_ptr.hpp>
+diff --git a/src/compress_gtf.cpp b/src/compress_gtf.cpp
+index a2cd10a..a3796fd 100644
+--- a/src/compress_gtf.cpp
++++ b/src/compress_gtf.cpp
+@@ -159,7 +159,7 @@ void compress_genes(FILE* ftranscripts,
+ vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i];
+ vector<Scaffold> gene_scaffs;
+ string gene_id;
+- foreach (shared_ptr<Scaffold> s, gene)
++ for_each (shared_ptr<Scaffold> s, gene)
+ {
+ if (gene_id == "")
+ gene_id = s->annotated_gene_id();
+@@ -175,7 +175,7 @@ void compress_genes(FILE* ftranscripts,
+ Scaffold smashed_gene;
+ if (!proj_intersection && !proj_union)
+ {
+- foreach (shared_ptr<Scaffold> s, gene)
++ for_each (shared_ptr<Scaffold> s, gene)
+ {
+ /*
+ *transfrag,
+@@ -224,7 +224,7 @@ void compress_genes(FILE* ftranscripts,
+ int gmax = -1;
+ int gmin = numeric_limits<int>::max();
+
+- foreach (shared_ptr<Scaffold> s, gene)
++ for_each (shared_ptr<Scaffold> s, gene)
+ {
+ //iso_ops.push_back(s->augmented_ops());
+ //sort (iso_ops.back().begin(), iso_ops.back().end());
+@@ -234,7 +234,7 @@ void compress_genes(FILE* ftranscripts,
+ gmax = s->right();
+ }
+
+- foreach (shared_ptr<Scaffold> s, gene)
++ for_each (shared_ptr<Scaffold> s, gene)
+ {
+ if (s->left() > gmin)
+ {
+@@ -347,7 +347,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* gtf_out)
+ vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table;
+ vector<pair<string, vector<double> > > sample_count_table;
+
+- foreach (FILE* ref_gtf, ref_gtf_files)
++ for_each (FILE* ref_gtf, ref_gtf_files)
+ {
+ vector<shared_ptr<Scaffold> > ref_mRNAs;
+ ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true);
+@@ -393,7 +393,7 @@ int main(int argc, char** argv)
+
+ vector<FILE*> ref_gtf_files;
+
+- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames)
++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames)
+ {
+ FILE* ref_gtf = NULL;
+ if (ref_gtf_in_filename != "")
+diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp
+index 575b064..7725910 100644
+--- a/src/cuffdiff.cpp
++++ b/src/cuffdiff.cpp
+@@ -490,7 +490,7 @@ void print_FPKM_tracking(FILE* fout,
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ AbundanceStatus status = NUMERIC_OK;
+- foreach (const FPKMContext& c, fpkms)
++ for_each (const FPKMContext& c, fpkms)
+ {
+ if (c.status == NUMERIC_FAIL)
+ status = NUMERIC_FAIL;
+@@ -811,7 +811,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ ::load_ref_rnas(mask_gtf, rt, mask_rnas, false, false);
+ }
+
+- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
+ {
+ fac->set_ref_rnas(ref_mRNAs);
+ if (mask_gtf)
+@@ -826,7 +826,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ int tmp_max_frag_len = 0;
+
+ ProgressBar p_bar("Inspecting maps and determining fragment length distributions.",0);
+- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
+ {
+ #if ENABLE_THREADS
+ while(1)
+@@ -877,7 +877,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ {
+ long double total_mass = 0.0;
+ long double total_norm_mass = 0.0;
+- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups)
++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups)
+ {
+ total_mass += rg->total_map_mass();
+ total_norm_mass += rg->normalized_map_mass();
+@@ -886,7 +886,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ if (total_mass > 0)
+ {
+ double scaling_factor = total_mass / total_norm_mass;
+- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups)
++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups)
+ {
+ double scaled_mass = scaling_factor * rg->normalized_map_mass();
+
+@@ -916,7 +916,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+
+ if (most_reps != 1 && poisson_dispersion == false)
+ {
+- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
+ {
+ if (fac->num_replicates() == 1)
+ {
+@@ -990,7 +990,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ shared_ptr<MassDispersionModel const> disperser;
+ disperser = fit_dispersion_model("pooled", scale_factors, sample_count_table);
+
+- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
+ {
+ rg_props->mass_dispersion_model(disperser);
+ }
+@@ -999,7 +999,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+
+ long double total_norm_mass = 0.0;
+ long double total_mass = 0.0;
+- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
+ {
+ total_norm_mass += rg_props->normalized_map_mass();
+ total_mass += rg_props->total_map_mass();
+@@ -1007,7 +1007,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+
+ // scale the normalized masses so that both quantile total count normalization
+ // are roughly on the same numerical scale
+- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
+ {
+ long double new_norm = rg_props->normalized_map_mass() * (total_mass / total_norm_mass);
+ rg_props->normalized_map_mass(new_norm);
+@@ -1039,7 +1039,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >());
+ quantitate_next_locus(rt, bundle_factories, test_launcher);
+ bool more_loci_remain = false;
+- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
+ {
+ if (rep_fac->bundles_remain())
+ {
+@@ -1071,7 +1071,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ }
+ }
+
+- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
+ {
+ rep_fac->reset();
+ }
+@@ -1081,9 +1081,9 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ if (corr_bias)
+ {
+ p_bar = ProgressBar("Learning bias parameters.", 0);
+- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
+ {
+- foreach (shared_ptr<BundleFactory> fac, rep_fac->factories())
++ for_each (shared_ptr<BundleFactory> fac, rep_fac->factories())
+ {
+ #if ENABLE_THREADS
+ while(1)
+@@ -1124,7 +1124,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ boost::this_thread::sleep(boost::posix_time::milliseconds(5));
+ }
+ #endif
+- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
+ {
+ rep_fac->reset();
+ }
+@@ -1167,7 +1167,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
+ //shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >());
+ quantitate_next_locus(rt, bundle_factories, test_launcher);
+ bool more_loci_remain = false;
+- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
+ {
+ if (rep_fac->bundles_remain())
+ {
+diff --git a/src/cufflinks.cpp b/src/cufflinks.cpp
+index 796af98..1030ae8 100644
+--- a/src/cufflinks.cpp
++++ b/src/cufflinks.cpp
+@@ -471,7 +471,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs,
+ {
+ for(size_t l = 0; l < lhs.size(); ++l)
+ {
+- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
+ {
+ // if we're past all the overlaps, just stop
+ if (ref_scaff->left() >= lhs[l].right() + overhang_3)
+@@ -504,7 +504,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs,
+ }
+ for(size_t r = 0; r < rhs.size(); ++r)
+ {
+- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
+ {
+ if (ref_scaff->left() >= rhs[r].right() + overhang_3)
+ {
+@@ -665,7 +665,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle,
+ if (ref_guided && enable_faux_reads && !hits.empty())
+ {
+ vector<Scaffold> pseudohits;
+- foreach(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
++ for_each(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
+ {
+ ref_scaff->tile_with_scaffs(pseudohits, tile_len, tile_off);
+ }
+@@ -842,7 +842,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle,
+ }
+ if (assembled_successfully)
+ {
+- foreach(Scaffold& scaff, tmp_scaffs)
++ for_each(Scaffold& scaff, tmp_scaffs)
+ {
+ scaffolds.push_back(shared_ptr<Scaffold>(new Scaffold(scaff)));
+ }
+@@ -886,7 +886,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+
+ // need the avg read length for depth of coverage calculation
+ double avg_read_length = 0;
+- foreach (MateHit& hit, hits_in_cluster)
++ for_each (MateHit& hit, hits_in_cluster)
+ {
+ if (hit.left_alignment())
+ avg_read_length += hit.left_alignment()->read_len();
+@@ -905,7 +905,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ }
+ else
+ {
+- foreach(shared_ptr<Abundance> ab, transfrag_cluster.abundances())
++ for_each(shared_ptr<Abundance> ab, transfrag_cluster.abundances())
+ {
+ ab->status(NUMERIC_HI_DATA);
+ }
+@@ -939,7 +939,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ {
+ shared_ptr<Abundance> ab_i = abundances[i];
+ bool found = false;
+- foreach (shared_ptr<Abundance> ab_j, filtered_transcripts)
++ for_each (shared_ptr<Abundance> ab_j, filtered_transcripts)
+ {
+ if (ab_i == ab_j)
+ {
+@@ -961,7 +961,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ transfrags_by_strand);
+
+
+- foreach (const AbundanceGroup& strand_group, transfrags_by_strand)
++ for_each (const AbundanceGroup& strand_group, transfrags_by_strand)
+ {
+ vector<AbundanceGroup> transfrags_by_gene;
+
+@@ -974,7 +974,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ cluster_transcripts<ConnectByExonOverlap>(strand_group, transfrags_by_gene);
+ }
+
+- foreach(const AbundanceGroup& gene, transfrags_by_gene)
++ for_each(const AbundanceGroup& gene, transfrags_by_gene)
+ {
+ const vector<shared_ptr<Abundance> >& iso_abundances = gene.abundances();
+ vector<Isoform> isoforms;
+@@ -985,7 +985,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ string ref_gene_id = "";
+
+ double major_isoform_FPKM = 0;
+- foreach (shared_ptr<Abundance> iso_ab, iso_abundances)
++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances)
+ {
+ if (iso_ab->transfrag()->is_ref())
+ {
+@@ -1002,7 +1002,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
+ major_isoform_FPKM = max(iso_ab->FPKM(), major_isoform_FPKM);
+ }
+
+- foreach (shared_ptr<Abundance> iso_ab, iso_abundances)
++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances)
+ {
+ // Calculate transcript depth of coverage and FMI from FPKM
+ double FPKM = iso_ab->FPKM();
+@@ -1067,7 +1067,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
+ {
+ vector<Scaffold> c;
+ scaffolds[i]->get_complete_subscaffolds(c);
+- foreach (Scaffold& s, c)
++ for_each (Scaffold& s, c)
+ {
+ split_partials.push_back(shared_ptr<Scaffold>(new Scaffold(s)));
+ }
+@@ -1076,7 +1076,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
+ scaffolds = split_partials;
+
+ vector<shared_ptr<Abundance> > abundances;
+- foreach(shared_ptr<Scaffold> s, scaffolds)
++ for_each(shared_ptr<Scaffold> s, scaffolds)
+ {
+ TranscriptAbundance* pT = new TranscriptAbundance;
+ pT->transfrag(s);
+@@ -1091,7 +1091,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
+ cluster_transcripts<ConnectByExonOverlap>(transfrags,
+ transfrags_by_cluster);
+
+- foreach(AbundanceGroup& cluster, transfrags_by_cluster)
++ for_each(AbundanceGroup& cluster, transfrags_by_cluster)
+ {
+ quantitate_transcript_cluster(cluster, total_map_mass, genes, bundle_too_large);
+ }
+@@ -1233,10 +1233,10 @@ void assemble_bundle(const RefSequenceTable& rt,
+ if (init_bundle_mode == REF_GUIDED)
+ {
+ hit_introns = new set<AugmentedCuffOp>();
+- foreach(const MateHit& h, bundle.non_redundant_hits())
++ for_each(const MateHit& h, bundle.non_redundant_hits())
+ {
+ Scaffold s(h);
+- foreach (AugmentedCuffOp a, s.augmented_ops())
++ for_each (AugmentedCuffOp a, s.augmented_ops())
+ {
+ if (a.opcode == CUFF_INTRON)
+ {
+@@ -1567,7 +1567,7 @@ void driver(const string& hit_file_name, FILE* ref_gtf, FILE* mask_gtf)
+ verbose_msg("%d ReadHits still live\n", num_deleted);
+ verbose_msg("Found %lu reference contigs\n", rt.size());
+
+- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
+ {
+ ref_scaff->clear_hits();
+ }
+diff --git a/src/differential.cpp b/src/differential.cpp
+index 3e5cff0..6b108cb 100644
+--- a/src/differential.cpp
++++ b/src/differential.cpp
+@@ -84,7 +84,7 @@ void TestLauncher::abundance_avail(const string& locus_id,
+ // acquire the lock itself.
+ bool TestLauncher::all_samples_reported_in(vector<shared_ptr<SampleAbundances> >& abundances)
+ {
+- foreach (shared_ptr<SampleAbundances> ab, abundances)
++ for_each (shared_ptr<SampleAbundances> ab, abundances)
+ {
+ if (!ab)
+ {
+@@ -436,7 +436,7 @@ pair<int, SampleDiffs::iterator> get_de_tests(const string& description,
+ // ublas::vector<double> null_kappa_mean;
+ // null_kappa_mean = ublas::zero_vector<double>(curr_kappa_cov.size1());
+ //
+-// foreach(ublas::vector<double>& sample, samples)
++// for_each(ublas::vector<double>& sample, samples)
+ // {
+ // null_kappa_mean += sample;
+ // }
+@@ -1056,7 +1056,7 @@ void sample_abundance_worker(const string& locus_tag,
+ {
+ vector<shared_ptr<Abundance> > abundances;
+
+- foreach(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds())
++ for_each(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds())
+ {
+ TranscriptAbundance* pT = new TranscriptAbundance;
+ pT->transfrag(s);
+@@ -1082,7 +1082,7 @@ void sample_abundance_worker(const string& locus_tag,
+ }
+ else
+ {
+- foreach(shared_ptr<Abundance> ab, abundances)
++ for_each(shared_ptr<Abundance> ab, abundances)
+ {
+ ab->status(NUMERIC_HI_DATA);
+ }
+@@ -1093,7 +1093,7 @@ void sample_abundance_worker(const string& locus_tag,
+ cluster_transcripts<ConnectByAnnotatedGeneId>(sample.transcripts,
+ transcripts_by_gene_id);
+
+- foreach(AbundanceGroup& ab_group, transcripts_by_gene_id)
++ for_each(AbundanceGroup& ab_group, transcripts_by_gene_id)
+ {
+ ab_group.locus_tag(locus_tag);
+ set<string> gene_ids = ab_group.gene_id();
+@@ -1119,7 +1119,7 @@ void sample_abundance_worker(const string& locus_tag,
+ &cds_count_cov,
+ &cds_fpkm_cov,
+ &cds_gamma_boot_cov);
+- foreach(AbundanceGroup& ab_group, transcripts_by_cds)
++ for_each(AbundanceGroup& ab_group, transcripts_by_cds)
+ {
+ ab_group.locus_tag(locus_tag);
+ set<string> protein_ids = ab_group.protein_id();
+@@ -1135,7 +1135,7 @@ void sample_abundance_worker(const string& locus_tag,
+ vector<shared_ptr<Abundance> > cds_abundances;
+ double max_cds_mass_variance = 0.0;
+ set<shared_ptr<ReadGroupProperties const> > rg_props;
+- foreach (AbundanceGroup& ab_group, sample.cds)
++ for_each (AbundanceGroup& ab_group, sample.cds)
+ {
+ cds_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group)));
+ max_cds_mass_variance = max(ab_group.max_mass_variance(), max_cds_mass_variance);
+@@ -1155,7 +1155,7 @@ void sample_abundance_worker(const string& locus_tag,
+ cluster_transcripts<ConnectByAnnotatedGeneId>(cds,
+ cds_by_gene);
+
+- foreach(AbundanceGroup& ab_group, cds_by_gene)
++ for_each(AbundanceGroup& ab_group, cds_by_gene)
+ {
+ ab_group.locus_tag(locus_tag);
+ set<string> gene_ids = ab_group.gene_id();
+@@ -1185,7 +1185,7 @@ void sample_abundance_worker(const string& locus_tag,
+ &tss_gamma_boot_cov);
+
+
+- foreach(AbundanceGroup& ab_group, transcripts_by_tss)
++ for_each(AbundanceGroup& ab_group, transcripts_by_tss)
+ {
+ ab_group.locus_tag(locus_tag);
+ set<string> tss_ids = ab_group.tss_id();
+@@ -1202,7 +1202,7 @@ void sample_abundance_worker(const string& locus_tag,
+ // Group TSS clusters by gene
+ vector<shared_ptr<Abundance> > primary_transcript_abundances;
+ set<shared_ptr<ReadGroupProperties const> > rg_props;
+- foreach (AbundanceGroup& ab_group, sample.primary_transcripts)
++ for_each (AbundanceGroup& ab_group, sample.primary_transcripts)
+ {
+ primary_transcript_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group)));
+ max_tss_mass_variance = max(max_tss_mass_variance, ab_group.max_mass_variance());
+@@ -1223,13 +1223,13 @@ void sample_abundance_worker(const string& locus_tag,
+ cluster_transcripts<ConnectByAnnotatedGeneId>(primary_transcripts,
+ primary_transcripts_by_gene);
+
+- foreach(AbundanceGroup& ab_group, primary_transcripts_by_gene)
++ for_each(AbundanceGroup& ab_group, primary_transcripts_by_gene)
+ {
+ ab_group.locus_tag(locus_tag);
+ set<string> gene_ids = ab_group.gene_id();
+ // if (gene_ids.size() > 1)
+ // {
+-// foreach (string st, gene_ids)
++// for_each (string st, gene_ids)
+ // {
+ // fprintf(stderr, "%s\n", st.c_str());
+ // }
+@@ -1314,7 +1314,7 @@ void sample_worker(const RefSequenceTable& rt,
+ bool perform_cds_analysis = final_est_run;
+ bool perform_tss_analysis = final_est_run;
+
+- foreach(shared_ptr<Scaffold> s, bundle.ref_scaffolds())
++ for_each(shared_ptr<Scaffold> s, bundle.ref_scaffolds())
+ {
+ if (s->annotated_tss_id() == "")
+ {
+@@ -1439,7 +1439,7 @@ void sample_worker(const RefSequenceTable& rt,
+ ///////////////////////////////////////////////
+
+
+- foreach(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds())
++ for_each(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds())
+ {
+ ref_scaff->clear_hits();
+ }
+@@ -1465,7 +1465,7 @@ void dump_locus_variance_info(const string& filename)
+
+ fprintf(fdump,
+ "condition\tdescription\tlocus_counts\tempir_var\tlocus_fit_var\tsum_iso_fit_var\tcross_replicate_js\tnum_transcripts\tbayes_gamma_trace\tempir_gamma_trace\tcount_mean\tgamma_var\tgamma_bootstrap_var\tlocus_salient_frags\tlocus_total_frags\tcount_sharing\n");
+- foreach (LocusVarianceInfo& L, locus_variance_info_table)
++ for_each (LocusVarianceInfo& L, locus_variance_info_table)
+ {
+ for (size_t i = 0; i < L.gamma.size(); ++i)
+ {
+@@ -1503,22 +1503,22 @@ void test_differential(const string& locus_tag,
+ for (size_t i = 0; i < samples.size(); ++i)
+ {
+ const AbundanceGroup& ab_group = samples[i]->transcripts;
+- foreach (shared_ptr<Abundance> ab, ab_group.abundances())
++ for_each (shared_ptr<Abundance> ab, ab_group.abundances())
+ {
+ add_to_tracking_table(i, *ab, tracking.isoform_fpkm_tracking);
+ }
+
+- foreach (AbundanceGroup& ab, samples[i]->cds)
++ for_each (AbundanceGroup& ab, samples[i]->cds)
+ {
+ add_to_tracking_table(i, ab, tracking.cds_fpkm_tracking);
+ }
+
+- foreach (AbundanceGroup& ab, samples[i]->primary_transcripts)
++ for_each (AbundanceGroup& ab, samples[i]->primary_transcripts)
+ {
+ add_to_tracking_table(i, ab, tracking.tss_group_fpkm_tracking);
+ }
+
+- foreach (AbundanceGroup& ab, samples[i]->genes)
++ for_each (AbundanceGroup& ab, samples[i]->genes)
+ {
+ add_to_tracking_table(i, ab, tracking.gene_fpkm_tracking);
+ }
+diff --git a/src/filters.cpp b/src/filters.cpp
+index 0a10b50..5ab31e0 100644
+--- a/src/filters.cpp
++++ b/src/filters.cpp
+@@ -752,7 +752,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
+
+ if (library_type != "transfrags")
+ {
+- foreach (Scaffold& scaff, scaffolds)
++ for_each (Scaffold& scaff, scaffolds)
+ {
+ if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV))
+ continue;
+@@ -761,7 +761,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
+ vector<double> coverage(scaff_len, 0.0);
+
+ double total = 0;
+- foreach(const MateHit* hit, scaff.mate_hits())
++ for_each(const MateHit* hit, scaff.mate_hits())
+ {
+ int start, end, frag_len;
+ if (!scaff.map_frag(*hit, start, end, frag_len)) continue;
+@@ -906,7 +906,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
+ }
+ else
+ {
+- foreach (Scaffold& scaff, scaffolds)
++ for_each (Scaffold& scaff, scaffolds)
+ {
+ if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV))
+ continue;
+@@ -915,7 +915,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
+ vector<double> coverage(scaff_len, 0.0);
+
+ double total = 0;
+- foreach(const MateHit* hit, scaff.mate_hits())
++ for_each(const MateHit* hit, scaff.mate_hits())
+ {
+ int start, end, frag_len;
+ if (!scaff.map_frag(*hit, start, end, frag_len)) continue;
+diff --git a/src/genes.h b/src/genes.h
+index 4dfa996..eb48a14 100644
+--- a/src/genes.h
++++ b/src/genes.h
+@@ -169,7 +169,7 @@ public:
+
+ bool has_ref_trans() const
+ {
+- foreach (const Isoform& iso, _isoforms)
++ for_each (const Isoform& iso, _isoforms)
+ {
+ if (iso.is_ref_trans())
+ return true;
+@@ -180,7 +180,7 @@ public:
+ double estimated_count() const
+ {
+ double est = 0.0;
+- foreach (const Isoform& iso, _isoforms)
++ for_each (const Isoform& iso, _isoforms)
+ {
+ est += iso.estimated_count();
+ }
+@@ -191,7 +191,7 @@ public:
+ {
+ double eff = 0.0;
+ double total_fpkm = 0;
+- foreach (const Isoform& iso, _isoforms)
++ for_each (const Isoform& iso, _isoforms)
+ {
+ eff += iso.FPKM() * iso.effective_length();
+ total_fpkm += iso.FPKM();
+diff --git a/src/gtf_to_sam.cpp b/src/gtf_to_sam.cpp
+index 12f70c1..f52d40a 100644
+--- a/src/gtf_to_sam.cpp
++++ b/src/gtf_to_sam.cpp
+@@ -241,13 +241,13 @@ void set_relative_fpkms(vector<shared_ptr<Scaffold> >& ref_mRNAs)
+ vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i];
+
+ double total_fpkm = 0.0;
+- foreach(shared_ptr<Scaffold> scaff, gene)
++ for_each(shared_ptr<Scaffold> scaff, gene)
+ {
+ total_fpkm += scaff->fpkm();
+ }
+ if (total_fpkm > 0)
+ {
+- foreach (shared_ptr<Scaffold> scaff, gene)
++ for_each (shared_ptr<Scaffold> scaff, gene)
+ {
+ scaff->fpkm(scaff->fpkm() / total_fpkm);
+ }
+@@ -263,7 +263,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* sam_out)
+ vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table;
+ vector<pair<string, vector<double> > > sample_count_table;
+
+- foreach (FILE* ref_gtf, ref_gtf_files)
++ for_each (FILE* ref_gtf, ref_gtf_files)
+ {
+ vector<shared_ptr<Scaffold> > ref_mRNAs;
+ ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true);
+@@ -314,7 +314,7 @@ int main(int argc, char** argv)
+
+ vector<FILE*> ref_gtf_files;
+
+- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames)
++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames)
+ {
+ FILE* ref_gtf = NULL;
+ if (ref_gtf_in_filename != "")
+diff --git a/src/hits.cpp b/src/hits.cpp
+index 910ba0f..dc81813 100644
+--- a/src/hits.cpp
++++ b/src/hits.cpp
+@@ -233,7 +233,7 @@ void collapse_hits(const vector<MateHit>& hits,
+ non_redundant.erase(new_end, non_redundant.end());
+ non_redundant.resize(non_redundant.size());
+
+- foreach(MateHit& hit, non_redundant)
++ for_each(MateHit& hit, non_redundant)
+ hit.collapse_mass(0);
+
+ size_t curr_aln = 0;
+@@ -252,7 +252,7 @@ void collapse_hits(const vector<MateHit>& hits,
+ ++curr_aln;
+ }
+
+- //foreach(MateHit& hit, non_redundant)
++ //for_each(MateHit& hit, non_redundant)
+ //assert(hit.collapse_mass() <= 1 || !hit.is_multi());
+
+ //non_redundant.erase(remove_if(non_redundant.begin(),non_redundant.end(),has_no_collapse_mass), non_redundant.end());
+diff --git a/src/replicates.cpp b/src/replicates.cpp
+index 634f209..ec8ce9c 100644
+--- a/src/replicates.cpp
++++ b/src/replicates.cpp
+@@ -236,7 +236,7 @@ fit_dispersion_model_helper(const string& condition_name,
+ mean /= p.counts.size();
+
+ double var = 0.0;
+- foreach (double d, p.counts)
++ for_each (double d, p.counts)
+ {
+ var += (d - mean) * (d - mean);
+ }
+@@ -363,7 +363,7 @@ fit_dispersion_model(const string& condition_name,
+ ProgressBar p_bar("Modeling fragment count overdispersion.",0);
+
+ int max_transcripts = 0;
+- foreach(const LocusCountList& L, sample_count_table)
++ for_each(const LocusCountList& L, sample_count_table)
+ {
+ if (L.num_transcripts > max_transcripts)
+ {
+@@ -382,7 +382,7 @@ fit_dispersion_model(const string& condition_name,
+ if (i != 0)
+ {
+ // vector<LocusCountList> sample_count_subtable;
+-// foreach(const LocusCountList& L, sample_count_table)
++// for_each(const LocusCountList& L, sample_count_table)
+ // {
+ // if (L.num_transcripts == i)
+ // {
+diff --git a/src/replicates.h b/src/replicates.h
+index ca4484f..73d339c 100644
+--- a/src/replicates.h
++++ b/src/replicates.h
+@@ -99,7 +99,7 @@ public:
+ #if ENABLE_THREADS
+ boost::mutex::scoped_lock lock(_rep_factory_lock);
+ #endif
+- foreach (boost::shared_ptr<BundleFactory> fac, _factories)
++ for_each (boost::shared_ptr<BundleFactory> fac, _factories)
+ {
+ if (fac->bundles_remain())
+ return true;
+@@ -115,7 +115,7 @@ public:
+ std::vector<HitBundle*> bundles;
+
+ bool non_empty_bundle = false;
+- foreach (boost::shared_ptr<BundleFactory> fac, _factories)
++ for_each (boost::shared_ptr<BundleFactory> fac, _factories)
+ {
+ bundles.push_back(new HitBundle());
+ if (fac->next_bundle(*(bundles.back())))
+@@ -126,7 +126,7 @@ public:
+
+ if (non_empty_bundle == false)
+ {
+- foreach (HitBundle* in_bundle, bundles)
++ for_each (HitBundle* in_bundle, bundles)
+ {
+ in_bundle->ref_scaffolds().clear();
+ in_bundle->clear_hits();
+@@ -149,7 +149,7 @@ public:
+ // Merge the replicates into a combined bundle of hits.
+ HitBundle::combine(bundles, bundle_out);
+
+- foreach (HitBundle* in_bundle, bundles)
++ for_each (HitBundle* in_bundle, bundles)
+ {
+ in_bundle->ref_scaffolds().clear();
+ in_bundle->clear_hits();
+@@ -163,7 +163,7 @@ public:
+ #if ENABLE_THREADS
+ boost::mutex::scoped_lock lock(_rep_factory_lock);
+ #endif
+- foreach (shared_ptr<BundleFactory> fac, _factories)
++ for_each (shared_ptr<BundleFactory> fac, _factories)
+ {
+ fac->reset();
+ }
+@@ -246,7 +246,7 @@ public:
+ shared_ptr<MassDispersionModel const> disperser;
+ disperser = fit_dispersion_model(_condition_name,scale_factors, sample_count_table);
+
+- foreach (shared_ptr<BundleFactory> fac, _factories)
++ for_each (shared_ptr<BundleFactory> fac, _factories)
+ {
+ shared_ptr<ReadGroupProperties> rg_props = fac->read_group_properties();
+ rg_props->mass_dispersion_model(disperser);
+@@ -260,7 +260,7 @@ public:
+ #if ENABLE_THREADS
+ boost::mutex::scoped_lock lock(_rep_factory_lock);
+ #endif
+- foreach(shared_ptr<BundleFactory> fac, _factories)
++ for_each(shared_ptr<BundleFactory> fac, _factories)
+ {
+ fac->set_ref_rnas(mRNAs);
+ }
+@@ -271,7 +271,7 @@ public:
+ #if ENABLE_THREADS
+ boost::mutex::scoped_lock lock(_rep_factory_lock);
+ #endif
+- foreach(shared_ptr<BundleFactory> fac, _factories)
++ for_each(shared_ptr<BundleFactory> fac, _factories)
+ {
+ fac->set_mask_rnas(mRNAs);
+ }
+@@ -284,7 +284,7 @@ public:
+ #if ENABLE_THREADS
+ boost::mutex::scoped_lock lock(_rep_factory_lock);
+ #endif
+- foreach(shared_ptr<BundleFactory>& fac, _factories)
++ for_each(shared_ptr<BundleFactory>& fac, _factories)
+ {
+ fac->read_group_properties()->mass_dispersion_model(disperser);
+ }
+diff --git a/src/scaffolds.cpp b/src/scaffolds.cpp
+index 096f58a..c12118e 100644
+--- a/src/scaffolds.cpp
++++ b/src/scaffolds.cpp
+@@ -620,7 +620,7 @@ void Scaffold::tile_with_scaffs(vector<Scaffold>& tile_scaffs, int max_len, int
+
+ // genomic_offset actually could be zero - from an exon starting at coord
+ // 1 in some chromosome of the ref.
+-// foreach(const AugmentedCuffOp& op, ops)
++// for_each(const AugmentedCuffOp& op, ops)
+ // {
+ // assert (op.genomic_offset != 0);
+ // }
+@@ -819,7 +819,7 @@ void Scaffold::merge(const vector<Scaffold>& s,
+ if (library_type == "transfrags")
+ {
+ double avg_fpkm = 0.0;
+- foreach (const Scaffold& sc, s)
++ for_each (const Scaffold& sc, s)
+ {
+ avg_fpkm += sc.fpkm();
+ }
+@@ -871,7 +871,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler)
+
+ vector<AugmentedCuffOp> tmp_filler = filler;
+
+- foreach(const AugmentedCuffOp& op, orig_ops)
++ for_each(const AugmentedCuffOp& op, orig_ops)
+ {
+ assert (op.g_left() < op.g_right());
+
+@@ -888,7 +888,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler)
+ AugmentedCuffOp::merge_ops(tmp_filler, padded_filler, false);
+
+ vector<AugmentedCuffOp> overlapping;
+- foreach (const AugmentedCuffOp& op, padded_filler)
++ for_each (const AugmentedCuffOp& op, padded_filler)
+ {
+ //if (left() <= op.g_left() && right() >= op.g_right()
+ if(::overlap_in_genome(op.g_left(),op.g_right(), left(), right())
+@@ -1630,7 +1630,7 @@ void Scaffold::get_complete_subscaffolds(vector<Scaffold>& complete)
+
+ // const vector<const MateHit*>& hits = known.mate_hits();
+ // bool contains_spliced_hit = false;
+- // foreach (const MateHit* h, hits)
++ // for_each (const MateHit* h, hits)
+ // {
+ // const ReadHit* left = h->left_alignment();
+ // const ReadHit* right = h->right_alignment();
+@@ -1670,7 +1670,7 @@ double Scaffold::internal_exon_coverage() const
+ int left = augmented_ops()[2].g_left();
+ int right = augmented_ops()[augmented_ops().size() - 3].g_right();
+ vector<bool> covered(right-left, 0);
+- foreach(const MateHit* h, mate_hits())
++ for_each(const MateHit* h, mate_hits())
+ {
+ if (::overlap_in_genome(h->left(),h->right(), left, right))
+ {
+@@ -1694,7 +1694,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con
+ if (has_intron())
+ return true;
+
+- foreach (const MateHit* h, mate_hits())
++ for_each (const MateHit* h, mate_hits())
+ {
+ if (h->strand() == strand())
+ return true;
+@@ -1704,7 +1704,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con
+ if (ref_scaffs == NULL)
+ return false;
+
+- foreach (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
++ for_each (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
+ {
+ if (ref_scaff->strand() == strand() && exons_overlap(*this, *ref_scaff))
+ return true;
+@@ -1729,10 +1729,10 @@ bool Scaffold::hits_support_introns() const
+ {
+ set<AugmentedCuffOp> hit_introns;
+ set<AugmentedCuffOp> scaffold_introns;
+- foreach(const MateHit* h, _mates_in_scaff)
++ for_each(const MateHit* h, _mates_in_scaff)
+ {
+ Scaffold s(*h);
+- foreach (AugmentedCuffOp a, s.augmented_ops())
++ for_each (AugmentedCuffOp a, s.augmented_ops())
+ {
+ if (a.opcode == CUFF_INTRON)
+ {
+@@ -1740,7 +1740,7 @@ bool Scaffold::hits_support_introns() const
+ }
+ }
+ }
+- foreach (AugmentedCuffOp a, _augmented_ops)
++ for_each (AugmentedCuffOp a, _augmented_ops)
+ {
+ if (a.opcode == CUFF_INTRON)
+ {
+@@ -1751,13 +1751,13 @@ bool Scaffold::hits_support_introns() const
+ if (hit_introns != scaffold_introns)
+ {
+ fprintf(stderr, "********************\n");
+- foreach(const AugmentedCuffOp& a, hit_introns)
++ for_each(const AugmentedCuffOp& a, hit_introns)
+ {
+ fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right());
+ }
+
+ fprintf(stderr, "####################\n");
+- foreach(const AugmentedCuffOp& a, scaffold_introns)
++ for_each(const AugmentedCuffOp& a, scaffold_introns)
+ {
+ fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right());
+ }
+@@ -1770,7 +1770,7 @@ bool Scaffold::hits_support_introns(set<AugmentedCuffOp>& hit_introns) const
+ {
+ set<AugmentedCuffOp> scaffold_introns;
+
+- foreach (AugmentedCuffOp a, _augmented_ops)
++ for_each (AugmentedCuffOp a, _augmented_ops)
+ {
+ if (a.opcode == CUFF_INTRON)
+ {
+diff --git a/src/scaffolds.h b/src/scaffolds.h
+index 0f29e80..f8410f7 100644
+--- a/src/scaffolds.h
++++ b/src/scaffolds.h
+@@ -314,7 +314,7 @@ public:
+ if (library_type == "transfrags")
+ {
+ double avg_fpkm = 0.0;
+- foreach (const Scaffold& sc, hits)
++ for_each (const Scaffold& sc, hits)
+ {
+ avg_fpkm += sc.fpkm();
+ }
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch
new file mode 100644
index 000000000000..360e9c1a11b8
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch
@@ -0,0 +1,20 @@
+ src/lemon/bits/base_extender.h | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/lemon/bits/base_extender.h b/src/lemon/bits/base_extender.h
+index 84bb242..b812247 100644
+--- a/src/lemon/bits/base_extender.h
++++ b/src/lemon/bits/base_extender.h
+@@ -359,10 +359,10 @@ namespace lemon {
+ }
+
+ Node source(const UEdge& edge) const {
+- return aNode(edge);
++ return this->aNode(edge);
+ }
+ Node target(const UEdge& edge) const {
+- return bNode(edge);
++ return this->bNode(edge);
+ }
+
+ void firstInc(UEdge& edge, bool& dir, const Node& node) const {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
new file mode 100644
index 000000000000..47784088fab9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
@@ -0,0 +1,28 @@
+ configure.ac | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 96ffbac..e88b8e4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
+
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ #echo "${host_cpu}-${host_os}"
+@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with
+ [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
+
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
+-CXXFLAGS="$CFLAGS"
+-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
+ user_LDFLAGS="$LDFLAGS"
+ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
new file mode 100644
index 000000000000..3b9abd812680
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
@@ -0,0 +1,16 @@
+ ax_bam.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ax_bam.m4 b/ax_bam.m4
+index 7d463b7..95f1bed 100644
+--- a/ax_bam.m4
++++ b/ax_bam.m4
+@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then
+ AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
+ fi
+ else
+- BAM_LIB="-lbam"
++ BAM_LIB="-lbam -lhts"
+ AC_SUBST(BAM_CPPFLAGS)
+ AC_SUBST(BAM_LDFLAGS)
+ AC_SUBST(BAM_LIB)
diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/cufflinks/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
new file mode 100644
index 000000000000..5c0e901d9aba
--- /dev/null
+++ b/sci-biology/cutg/Manifest
@@ -0,0 +1 @@
+DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
new file mode 100644
index 000000000000..46163bc2a80f
--- /dev/null
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Codon usage tables calculated from GenBank"
+HOMEPAGE="http://www.kazusa.or.jp/codon/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+ if use emboss; then
+ mkdir CODONS || die
+ ebegin "Indexing CUTG for usage with EMBOSS."
+ EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
+ "Indexing CUTG failed."
+ eend
+ fi
+}
+
+src_install() {
+ local file
+ dodoc README CODON_LABEL SPSUM_LABEL
+ if ! use minimal; then
+ dodir /usr/share/${PN}
+ mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \
+ "Installing raw CUTG database failed."
+ fi
+
+ if use emboss; then
+ dodir /usr/share/EMBOSS/data/CODONS
+ cd CODONS || die
+ for file in *; do
+ mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \
+ "Installing the EMBOSS-indexed database failed."
+ done
+ fi
+}
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
new file mode 100644
index 000000000000..59b110912ca6
--- /dev/null
+++ b/sci-biology/cutg/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ Codon usage tables maintained at the Kazusa DNA Research Institute.
+ Codon usage in individual genes has been calculated using the
+ nucleotide sequence data obtained from the GenBank Genetic Sequence
+ Database. The compilation of codon usage is synchronized with each
+ major release of GenBank.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
new file mode 100644
index 000000000000..de90a59afc93
--- /dev/null
+++ b/sci-biology/dialign-tx/Manifest
@@ -0,0 +1 @@
+DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
new file mode 100644
index 000000000000..c73d043742b8
--- /dev/null
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+MY_P=DIALIGN-TX_${PV}
+
+DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
+HOMEPAGE="http://dialign-tx.gobics.de/"
+SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+ sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \
+ -i source/Makefile || die #336533
+ epatch "${FILESDIR}"/${P}-implicits.patch
+}
+
+src_compile() {
+ emake -C source clean
+ emake -C source CC="$(tc-getCC)" \
+ CPPFLAGS=""
+}
+
+src_install() {
+ dobin "${S}"/source/dialign-tx
+ insinto /usr/$(get_libdir)/${PN}/conf
+ doins "${S}"/conf/*
+}
+
+pkg_postinst() {
+ einfo "The configuration directory is"
+ einfo "${ROOT}usr/$(get_libdir)/${PN}/conf"
+ einfo "You will need to pass this to ${PN} on every run."
+}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
new file mode 100644
index 000000000000..a8388d03232f
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
@@ -0,0 +1,18 @@
+--- source/museq.c
++++ source/museq.c
+@@ -38,6 +38,7 @@
+ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+ // struct prob_dist *pdist);
+ //extern struct diag_col *create_diag_col(int seq_amount);
++extern void free_diag(struct diag* dg);
+ extern void free_diag_col(struct diag_col* dcol);
+ extern struct diag_col *find_all_diags(struct scr_matrix *smatrix,
+ struct prob_dist *pdist,
+@@ -52,6 +53,7 @@
+
+ // alig.c
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
++extern void free_alignment(struct alignment *algn);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol,
+ struct scr_matrix* smatrix,
diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/dialign-tx/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest
new file mode 100644
index 000000000000..8f3f4080e56f
--- /dev/null
+++ b/sci-biology/dialign2/Manifest
@@ -0,0 +1 @@
+DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84
diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1.ebuild
new file mode 100644
index 000000000000..58557729b529
--- /dev/null
+++ b/sci-biology/dialign2/dialign2-2.2.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Multiple sequence alignment"
+HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign"
+SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}"/dialign_package
+
+src_compile() {
+ emake -C src \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS} -I. -DCONS -c"
+}
+
+src_install() {
+ dobin src/${PN}-2
+ insinto /usr/share/${PN}
+ doins dialign2_dir/*
+
+ cat >> "${T}"/80${PN} <<- EOF
+ DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}"
+ EOF
+ doenvd "${T}"/80${PN}
+}
diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml
new file mode 100644
index 000000000000..7bc6ee8ea837
--- /dev/null
+++ b/sci-biology/dialign2/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ <name>Justin Lecher</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest
new file mode 100644
index 000000000000..fe0ae5f610cb
--- /dev/null
+++ b/sci-biology/diya/Manifest
@@ -0,0 +1 @@
+DIST diya-1.0-rc4.tar.gz 386706 SHA256 13f7dd4dd7f96143948587884954e337552d7491347c2c174e786824880590c7
diff --git a/sci-biology/diya/diya-1.0_rc4.ebuild b/sci-biology/diya/diya-1.0_rc4.ebuild
new file mode 100644
index 000000000000..2211525f8af9
--- /dev/null
+++ b/sci-biology/diya/diya-1.0_rc4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module
+
+DESCRIPTION="Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation"
+HOMEPAGE="http://gmod.org/wiki/Diya"
+SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="-minimal"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="sci-biology/bioperl
+ dev-perl/Data-Utilities
+ dev-perl/XML-Simple"
+RDEPEND="${DEPEND}
+ !minimal? (
+ sci-biology/mummer
+ sci-biology/glimmer
+ sci-biology/trnascan-se
+ sci-biology/infernal )"
+
+# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++
+# * rfamscan.pl v0.1 (http://www.sanger.ac.uk/Users/sgj/code/)
+# * UniRef50 (http://www.ebi.ac.uk/uniref/)
+# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/)
+# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/.
+
+S="${WORKDIR}/diya-${PV/_/-}"
+
+SRC_TEST=do
+
+src_install() {
+ mydoc="INSTALL README docs/diya.html"
+ perl-module_src_install
+ insinto /usr/share/${PN}
+ doins -r diya.conf docs examples scripts
+}
diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml
new file mode 100644
index 000000000000..d6b9de8b20a7
--- /dev/null
+++ b/sci-biology/diya/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">diyg</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest
new file mode 100644
index 000000000000..60015030796d
--- /dev/null
+++ b/sci-biology/elph/Manifest
@@ -0,0 +1,2 @@
+DIST ELPH-0.1.5.tar.gz 153150 RMD160 7e60e2cf9a99cb435768cebbcd1506164e8a901c SHA1 1a3820c851ac0d021c9696ba1fd4eec819d82dbc SHA256 6ffa160f85cb2569bdf869cb0514dc624afcef4f2d8a36efbd1228d1a16cf361
+DIST ELPH-1.0.1.tar.gz 113476 RMD160 854bc34aba30f1c7493536e1b2e36dd8143af7e7 SHA1 9c8bf6ac54ade29daa15dc07aeeb94747626298a SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9
diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild
new file mode 100644
index 000000000000..5fc361ace8fd
--- /dev/null
+++ b/sci-biology/elph/elph-0.1.5.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
+LICENSE="Artistic"
+HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="x86"
+
+S="${WORKDIR}/ELPH/sources"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-usage.patch
+ sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" \
+ -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" \
+ -e "s/LINKER := g++/LINKER := $(tc-getCXX)/" \
+ Makefile || die "Failed to patch Makefile."
+}
+
+src_compile() {
+ make || die "Compilation failed."
+}
+
+src_install() {
+ dobin elph || die "Failed to install program."
+ cd "${WORKDIR}"/ELPH
+ dodoc VERSION || die "Documentation installation failed."
+ newdoc Readme.ELPH README || die "Readme installation failed."
+}
diff --git a/sci-biology/elph/elph-1.0.1.ebuild b/sci-biology/elph/elph-1.0.1.ebuild
new file mode 100644
index 000000000000..78476added83
--- /dev/null
+++ b/sci-biology/elph/elph-1.0.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
+LICENSE="Artistic"
+HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+S=${WORKDIR}/ELPH/sources
+
+src_compile() {
+ emake CC="$(tc-getCXX)" LINKER="$(tc-getCXX)" \
+ CFLAGS="${CXXFLAGS} -D_REENTRANT" LDFLAGS="${LDFLAGS}" || die
+}
+
+src_install() {
+ dobin elph || die "Failed to install program."
+ cd "${WORKDIR}"/ELPH
+ dodoc VERSION || die "Documentation installation failed."
+ newdoc Readme.ELPH README || die "Readme installation failed."
+}
diff --git a/sci-biology/elph/files/elph-0.1.4-usage.patch b/sci-biology/elph/files/elph-0.1.4-usage.patch
new file mode 100644
index 000000000000..be49e2d1ebb8
--- /dev/null
+++ b/sci-biology/elph/files/elph-0.1.4-usage.patch
@@ -0,0 +1,133 @@
+--- elph.cc~ 2003-06-03 14:45:22.000000000 -0400
++++ elph.cc 2004-10-30 10:14:49.220415168 -0400
+@@ -26,11 +26,11 @@
+ period variable\n\
+ -x : print maximum positions within sequences\n\
+ -g : find significance of motif\n\
+- -t <matrix> : test if there is significant difference between the two
+- input files for a given motif matrix; <matrix> is the file
++ -t <matrix> : test if there is significant difference between the two\n\
++ input files for a given motif matrix; <matrix> is the file\n\
+ containing the motif matrix\n\
+- -l : compute Least Likely Consensus (LLC) for given motif
+- -c : in conjunction with -m option: motif is not necessarily in
++ -l : compute Least Likely Consensus (LLC) for given motif\n\
++ -c : in conjunction with -m option: motif is not necessarily in\n\
+ the closest edit distance from input motif\n\
+ LEN=n : n = length of motif\n\
+ ITERNO=n : n = no of iterations to compute the global maximum;\n\
+@@ -41,7 +41,7 @@
+ default = 1000\n\
+ "
+
+-// global variables:
++// global variables:
+ int ITER_NO=10;
+ int MAX_LOOP=500;
+ int printmax=0;
+@@ -66,7 +66,7 @@
+ seqType t;
+
+ GArgs args(argc, argv, "ho:abglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO=");
+-
++
+ // == Process arguments.
+
+ int e;
+@@ -83,7 +83,7 @@
+
+ if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files
+
+- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
+ M->twofilesignif(gdet,testfile,SignifNo,print,pattern);
+
+ }
+@@ -93,11 +93,11 @@
+ // given motif
+
+ M = new Motif(infile,outf,t,pattern);
+- if(defLLC) {
++ if(defLLC) {
+ double llc=M->computeLLC(pattern,print);
+ fprintf(outf,"LLC = %f\n",llc);
+ }
+-
++
+ }
+ else {
+
+@@ -108,7 +108,7 @@
+ }
+
+ double globAlignProb;
+-
++
+ globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet);
+
+
+@@ -116,13 +116,13 @@
+ /*info=M->InfoPar(globAlignProb);
+ fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info);
+ M->printMotif();*/
+-
++
+ // optimizing
+ fprintf(stderr,"Optimizing...\n");
+ globAlignProb=M->optimize(globAlignProb,info,closest);
+ fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n");
+ fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb));
+-
++
+ if(runsignif) {
+ M->runforsignif(SignifNo,print,gdet,pattern);
+ }
+@@ -134,17 +134,17 @@
+
+ seqType Process_Options(GArgs* args)
+ {
+-
+- if (args->startNonOpt()) { //parse the non-options arguments
++
++ if (args->startNonOpt()) { //parse the non-options arguments
+ //(usually filenames)
+ infile=args->nextNonOpt();
+ }
+
+- if (infile.is_empty() || args->getOpt('h')!=NULL)
++ if (infile.is_empty() || args->getOpt('h')!=NULL)
+ GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input
+
+ testfile=args->nextNonOpt();
+-
++
+ GString outfile=args->getOpt('o');
+ if (!outfile.is_empty()) {
+ outf=fopen(outfile, "w");
+@@ -156,7 +156,7 @@
+ matrixfile=args->getOpt('t');
+
+ GString param;
+-
++
+ pattern=args->getOpt('m');
+ if(pattern.is_empty()) {
+ param=args->getOpt("LEN");
+@@ -200,7 +200,7 @@
+
+ seqType t;
+ if(args->getOpt('a')!=NULL) t=aac; else t=nucl;
+-
++
+ return(t);
+
+ }
+@@ -210,7 +210,7 @@
+ Motif *M;
+
+ double llcmax=-HUGE_VAL;
+- GString seed;
++ GString seed;
+ for(int i1=0;i1<4;i1++)
+ for(int i2=0;i2<4;i2++)
+ for(int i3=0;i3<4;i3++)
diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch
new file mode 100644
index 000000000000..139b83c1c1c6
--- /dev/null
+++ b/sci-biology/elph/files/elph-0.1.5-usage.patch
@@ -0,0 +1,133 @@
+--- elph.cc.old 2005-01-11 14:17:47.000000000 -0500
++++ elph.cc 2005-01-27 19:42:30.218350552 -0500
+@@ -26,11 +26,11 @@
+ period variable\n\
+ -x : print maximum positions within sequences\n\
+ -g : find significance of motif\n\
+- -t <matrix> : test if there is significant difference between the two
+- input files for a given motif matrix; <matrix> is the file
++ -t <matrix> : test if there is significant difference between the two\n\
++ input files for a given motif matrix; <matrix> is the file\n\
+ containing the motif matrix\n\
+- -l : compute Least Likely Consensus (LLC) for given motif
+- -c : in conjunction with -m option: motif is not necessarily in
++ -l : compute Least Likely Consensus (LLC) for given motif\n\
++ -c : in conjunction with -m option: motif is not necessarily in\n\
+ the closest edit distance from input motif\n\
+ LEN=n : n = length of motif\n\
+ ITERNO=n : n = no of iterations to compute the global maximum;\n\
+@@ -41,7 +41,7 @@
+ default = 1000\n\
+ "
+
+-// global variables:
++// global variables:
+ int ITER_NO=10;
+ int MAX_LOOP=500;
+ int printmax=0;
+@@ -66,7 +66,7 @@
+ seqType t;
+
+ GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO=");
+-
++
+ // == Process arguments.
+
+ int e;
+@@ -83,7 +83,7 @@
+
+ if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files
+
+- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
+ M->twofilesignif(gdet,testfile,SignifNo,print,pattern);
+
+ }
+@@ -93,11 +93,11 @@
+ // given motif
+
+ M = new Motif(infile,outf,t,pattern);
+- if(defLLC) {
++ if(defLLC) {
+ double llc=M->computeLLC(pattern,print);
+ fprintf(outf,"LLC = %f\n",llc);
+ }
+-
++
+ }
+ else {
+
+@@ -108,7 +108,7 @@
+ }
+
+ double globAlignProb;
+-
++
+ globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet);
+
+
+@@ -116,13 +116,13 @@
+ /*info=M->InfoPar(globAlignProb);
+ fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info);
+ M->printMotif();*/
+-
++
+ // optimizing
+ fprintf(stderr,"Optimizing...\n");
+ globAlignProb=M->optimize(globAlignProb,info,closest);
+ fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n");
+ fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb));
+-
++
+ if(runsignif) {
+ M->runforsignif(SignifNo,print,gdet,pattern);
+ }
+@@ -134,17 +134,17 @@
+
+ seqType Process_Options(GArgs* args)
+ {
+-
+- if (args->startNonOpt()) { //parse the non-options arguments
++
++ if (args->startNonOpt()) { //parse the non-options arguments
+ //(usually filenames)
+ infile=args->nextNonOpt();
+ }
+
+- if (infile.is_empty() || args->getOpt('h')!=NULL)
++ if (infile.is_empty() || args->getOpt('h')!=NULL)
+ GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input
+
+ testfile=args->nextNonOpt();
+-
++
+ GString outfile=args->getOpt('o');
+ if (!outfile.is_empty()) {
+ outf=fopen(outfile, "w");
+@@ -156,7 +156,7 @@
+ matrixfile=args->getOpt('t');
+
+ GString param;
+-
++
+ pattern=args->getOpt('m');
+ if(pattern.is_empty()) {
+ param=args->getOpt("LEN");
+@@ -200,7 +200,7 @@
+
+ seqType t;
+ if(args->getOpt('a')!=NULL) t=aac; else t=nucl;
+-
++
+ return(t);
+
+ }
+@@ -210,7 +210,7 @@
+ Motif *M;
+
+ double llcmax=-HUGE_VAL;
+- GString seed;
++ GString seed;
+ for(int i1=0;i1<4;i1++)
+ for(int i2=0;i2<4;i2++)
+ for(int i3=0;i3<4;i3++)
diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml
new file mode 100644
index 000000000000..469879ba8f5b
--- /dev/null
+++ b/sci-biology/elph/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
+ DNA or protein sequences. The program takes as input a set containing
+ anywhere from a few dozen to thousands of sequences, and searches
+ through them for the most common motif, assuming that each sequence
+ contains one copy of the motif.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest
new file mode 100644
index 000000000000..408037d6a1ec
--- /dev/null
+++ b/sci-biology/embassy-cbstools/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693
+DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
new file mode 100644
index 000000000000..b2f9738aa495
--- /dev/null
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Applications from the CBS group"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild
new file mode 100644
index 000000000000..ca1539905c99
--- /dev/null
+++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS wrappers for applications from the CBS group"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..d29310efcb47
--- /dev/null
+++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index a70d4d2..b8f5e79 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 824a03c..9db171d 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-cbstools/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
new file mode 100644
index 000000000000..43c85d868e12
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/Manifest
@@ -0,0 +1 @@
+DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
new file mode 100644
index 000000000000..620383da2eb0
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+=" sci-biology/clustal-omega"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
new file mode 100644
index 000000000000..5525d79b525f
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f12ed19..b143922 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 9135679..c201149 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest
new file mode 100644
index 000000000000..74ca98eecf1d
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-domainatrix-0.1.0.tar.gz 420983 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1
+DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild
new file mode 100644
index 000000000000..ee009ca052f0
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Protein domain analysis add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
new file mode 100644
index 000000000000..9734758ee2ad
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain analysis add-on package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..a932e1ebe21e
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index d16cc02..d327a0d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index d405d00..54be7ca 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest
new file mode 100644
index 000000000000..87fdc97be669
--- /dev/null
+++ b/sci-biology/embassy-domalign/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-domalign-0.1.0.tar.gz 462156 SHA256 c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a
+DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild
new file mode 100644
index 000000000000..8a0e7bb2de92
--- /dev/null
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Protein domain alignment add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
new file mode 100644
index 000000000000..b26dd2cb35df
--- /dev/null
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain alignment add-on package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..033ddf7b6535
--- /dev/null
+++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
@@ -0,0 +1,101 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 7 ++-----
+ 2 files changed, 9 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 693eb4d..dc0fda9 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 8785446..fe85f11 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${embprefix}/include \
+- -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ ../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-domalign/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest
new file mode 100644
index 000000000000..76709b452174
--- /dev/null
+++ b/sci-biology/embassy-domsearch/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-domsearch-0.1.0.tar.gz 470537 SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95
+DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild
new file mode 100644
index 000000000000..48f945c08d8a
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Protein domain search add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
new file mode 100644
index 000000000000..e9c4a6c48fd4
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain search add-on package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..d24857c8386d
--- /dev/null
+++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f0f97fa..d419d7d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 9829ebd..433a5c5 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ ../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-domsearch/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
new file mode 100644
index 000000000000..7c67122bbc0a
--- /dev/null
+++ b/sci-biology/embassy-emnu/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-emnu-1.05.tar.gz 390229 SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
+DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild
new file mode 100644
index 000000000000..3163cb635c4c
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
+
+RDEPEND="sys-libs/ncurses
+ ${RDEPEND}"
+
+DEPEND="sys-libs/ncurses
+ ${DEPEND}"
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
new file mode 100644
index 000000000000..ee617cddf7ca
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Simple menu of EMBOSS applications"
+EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+IUSE+=" ncurses"
+
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
new file mode 100644
index 000000000000..4e14bac1704a
--- /dev/null
+++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
@@ -0,0 +1,139 @@
+ configure.ac | 67 +++++++++++---------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 7 +++---
+ 3 files changed, 18 insertions(+), 58 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 7482ade..b815bdb 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+@@ -899,20 +864,16 @@ dnl fi
+
+
+ dnl emnu and mse only: uses curses
+-dnl Test if --with-curses is given
+-AC_ARG_WITH([curses],
+-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])])
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
+
+-AC_MSG_CHECKING([for curses])
+-
+-AS_IF([test "${with_curses}"],
+-[
+- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+- LDFLAGS="$LDFLAGS -L${with_curses}/lib"
++AS_IF([test "x$enable_curses" = "xyes"], [
++ PKG_CHECK_MODULES([NCURSES], [ncurses])
++ PKG_CHECK_MODULES([FORM], [form])
++ PKG_CHECK_MODULES([MENU], [menu])
+ ])
+
+-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"])
+-
+
+
+
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index b295079..330c76f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \
++ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ ../../../plplot/libeplplot.la -lmenu -lform $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB)
++ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-emnu/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
new file mode 100644
index 000000000000..ade72c4415f8
--- /dev/null
+++ b/sci-biology/embassy-esim4/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
+DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild
new file mode 100644
index 000000000000..927f8ab6a202
--- /dev/null
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
new file mode 100644
index 000000000000..470cb0b299cd
--- /dev/null
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..ead54c91b5f3
--- /dev/null
+++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 924220a..2c45f46 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 0620938..0304bb8 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-esim4/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
new file mode 100644
index 000000000000..1aeb5559decf
--- /dev/null
+++ b/sci-biology/embassy-hmmer/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-hmmer-2.3.2.tar.gz 565686 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258
+DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild
new file mode 100644
index 000000000000..a246730c4b22
--- /dev/null
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
+
+RDEPEND="~sci-biology/hmmer-2.3.2"
+
+src_install() {
+ embassy_src_install
+ insinto /usr/include/emboss/hmmer
+ doins src/*.h
+}
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
new file mode 100644
index 000000000000..871d512a172a
--- /dev/null
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Wrappers for HMMER - Biological sequence analysis with profile HMMs"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+="sci-biology/hmmer"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
new file mode 100644
index 000000000000..90c45632eada
--- /dev/null
+++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 037ca00..f539ab6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index dc789bc..5a8c38e 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-hmmer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
new file mode 100644
index 000000000000..6d689c8ee615
--- /dev/null
+++ b/sci-biology/embassy-iprscan/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-iprscan-4.3.1.tar.gz 339939 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
+DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
new file mode 100644
index 000000000000..f8e7380c017c
--- /dev/null
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="InterProScan motif detection add-on package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild
new file mode 100644
index 000000000000..2ed141470a13
--- /dev/null
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="InterProScan motif detection add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..8c8a1060e30f
--- /dev/null
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 9052ca5..c12c268 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 0afc96a..904b41a 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-iprscan/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
new file mode 100644
index 000000000000..13e38d3a79dd
--- /dev/null
+++ b/sci-biology/embassy-meme/Manifest
@@ -0,0 +1 @@
+DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
new file mode 100644
index 000000000000..bdbc70a3bab2
--- /dev/null
+++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Wrappers for MEME - Multiple Em for Motif Elicitation"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND+=" sci-biology/meme"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
new file mode 100644
index 000000000000..56f5814e1efa
--- /dev/null
+++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 391989f..d921f25 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1600399..9f28162 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-meme/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest
new file mode 100644
index 000000000000..f42b89771c56
--- /dev/null
+++ b/sci-biology/embassy-memenew/Manifest
@@ -0,0 +1,2 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-memenew-0.1.0.tar.gz 450102 SHA256 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636
diff --git a/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild
new file mode 100644
index 000000000000..58f3852fce08
--- /dev/null
+++ b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
+
+src_install() {
+ embassy_src_install
+ insinto /usr/include/emboss/meme
+ doins src/INCLUDE/*.h
+}
diff --git a/sci-biology/embassy-memenew/metadata.xml b/sci-biology/embassy-memenew/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-memenew/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-mira/Manifest b/sci-biology/embassy-mira/Manifest
new file mode 100644
index 000000000000..6229623c3b0e
--- /dev/null
+++ b/sci-biology/embassy-mira/Manifest
@@ -0,0 +1,2 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-mira-2.8.2.tar.gz 365566 SHA256 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1
diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild
new file mode 100644
index 000000000000..28e3d2587d1e
--- /dev/null
+++ b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Fragment assembly add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-mira/metadata.xml b/sci-biology/embassy-mira/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-mira/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
new file mode 100644
index 000000000000..15e2c00a0f43
--- /dev/null
+++ b/sci-biology/embassy-mse/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90
+DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b
diff --git a/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild
new file mode 100644
index 000000000000..8767aee8f8d3
--- /dev/null
+++ b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Screen Editor"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
+
+src_install() {
+ embassy_src_install
+ insinto /usr/include/emboss/mse
+ doins h/*.h
+}
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
new file mode 100644
index 000000000000..32b6410620e1
--- /dev/null
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
+EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+IUSE+=" ncurses"
+
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+
+src_install() {
+ autotools-utils_src_install
+ insinto /usr/include/emboss/mse
+ doins h/*.h
+}
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..c1095b266d60
--- /dev/null
+++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
@@ -0,0 +1,149 @@
+ ckit/Makefile.am | 2 +-
+ configure.ac | 67 +++++++++++---------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 6 ++---
+ 4 files changed, 18 insertions(+), 59 deletions(-)
+
+diff --git a/ckit/Makefile.am b/ckit/Makefile.am
+index f87b131..a670d2b 100644
+--- a/ckit/Makefile.am
++++ b/ckit/Makefile.am
+@@ -2,7 +2,7 @@
+
+ lib_LTLIBRARIES = libckit.la
+
+-AM_CPPFLAGS = -I../h
++AM_CPPFLAGS = -I$(top_srcdir)/h
+
+ CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
+ seqspec.c ttyinterface.c nextseqentry.c \
+diff --git a/configure.ac b/configure.ac
+index a20d488..eb208bf 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"],
+
+
+
+-dnl emnu and mse only: uses curses
+-dnl Test if --with-curses is given
+-AC_ARG_WITH([curses],
+- [AS_HELP_STRING([--with-curses],
+- [curses (or ncurses)])])
+-if test "${with_curses}" ; then
+-AC_MSG_CHECKING([for curses])
+-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-LDFLAGS="$LDFLAGS -L${with_curses}/lib"
+-fi
+-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses")
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
++
++AS_IF([test "x$enable_curses" = "xyes"], [
++ PKG_CHECK_MODULES([NCURSES], [ncurses])
++])
+
+
+
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index b44632a..84e89b5 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../h -I${embprefix}/include \
+- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \
+- $(NLINCLUDES)
++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \
+ $(XLIB)
+ else
+ LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
+- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-mse/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
new file mode 100644
index 000000000000..638f9da73ac0
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945
+DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild
new file mode 100644
index 000000000000..2bc4a956502f
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild
@@ -0,0 +1,14 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package"
+LICENSE="freedist"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
new file mode 100644
index 000000000000..18b8b33c91fb
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="The Phylogeny Inference Package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+LICENSE+=" freedist"
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
new file mode 100644
index 000000000000..1cba944094a2
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
@@ -0,0 +1,111 @@
+ configure.ac | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 7 ++-----
+ 3 files changed, 10 insertions(+), 48 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index e5bfaf1..09ed517 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1883ce9..fb1787f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${embprefix}/include \
+- -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ ../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest
new file mode 100644
index 000000000000..8e615337acb6
--- /dev/null
+++ b/sci-biology/embassy-signature/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-signature-0.1.0.tar.gz 574940 SHA256 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f
+DIST embassy-signature-0.1.650.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild
new file mode 100644
index 000000000000..83f7f8487ee8
--- /dev/null
+++ b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Protein signature add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild
new file mode 100644
index 000000000000..b70e05d76087
--- /dev/null
+++ b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein signature add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..32e4d684cbb3
--- /dev/null
+++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 2f5ddd0..827543f 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index d77e43c..849f17a 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-signature/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest
new file mode 100644
index 000000000000..7cd125ec2b29
--- /dev/null
+++ b/sci-biology/embassy-structure/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23
+DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03
diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild
new file mode 100644
index 000000000000..64b653083ff2
--- /dev/null
+++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="Protein structure add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild
new file mode 100644
index 000000000000..b6fcd9770e3b
--- /dev/null
+++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein structure add-on package"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..bdd9e37714e4
--- /dev/null
+++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
@@ -0,0 +1,100 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index ee482ef..e4af4b1 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 81ade5d..2ed0d14 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-structure/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest
new file mode 100644
index 000000000000..7da88ac0231b
--- /dev/null
+++ b/sci-biology/embassy-topo/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-topo-1.0.0.tar.gz 379929 SHA256 a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16
+DIST embassy-topo-2.0.650.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55
diff --git a/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild
new file mode 100644
index 000000000000..f0ffdd356594
--- /dev/null
+++ b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild
new file mode 100644
index 000000000000..dec34b9db31f
--- /dev/null
+++ b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Transmembrane protein display"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..3c37879de8c8
--- /dev/null
+++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
@@ -0,0 +1,110 @@
+ configure.ac | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am | 2 +-
+ src/Makefile.am | 6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 8eeb8ca..4fd28ac 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1cdb0b1..0e86a4b 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+- -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-topo/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest
new file mode 100644
index 000000000000..d7061f3dd813
--- /dev/null
+++ b/sci-biology/embassy-vienna/Manifest
@@ -0,0 +1,3 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db
+DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
new file mode 100644
index 000000000000..62f1626a26a4
--- /dev/null
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EBO_DESCRIPTION="Vienna RNA package - RNA folding"
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild
new file mode 100644
index 000000000000..49eac3cdc4d8
--- /dev/null
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EBOV="6.0.1"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of the Vienna RNA package - RNA folding"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
+ mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="amd64 ~ppc x86"
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
new file mode 100644
index 000000000000..5ce365ed5497
--- /dev/null
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
@@ -0,0 +1,108 @@
+ configure.ac | 49 +++++++------------------------------------------
+ src/Makefile.am | 7 +++----
+ 2 files changed, 10 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f5a4ecf..bbe0743 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -649,33 +649,6 @@ AS_CASE([${host_os}],
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1f5b756..e178914 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \
+ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \
+- $(NLINCLUDES) \
+- -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+
+ if ISSHARED
+@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ liboviennarna_la_LDFLAGS = $(LINKFLAGS)
++liboviennarna_la_LIBADD = -lajax
+
+ ovrnaalifold_SOURCES = vrnaalifold.c
+ ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
+@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \
+ $(XLIB)
+ else
+ LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
+- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-vienna/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/embassy/embassy-6.0.1.ebuild b/sci-biology/embassy/embassy-6.0.1.ebuild
new file mode 100644
index 000000000000..3c7c37b20ff6
--- /dev/null
+++ b/sci-biology/embassy/embassy-6.0.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
+HOMEPAGE="http://www.emboss.org/"
+SRC_URI=""
+LICENSE="GPL-2 freedist"
+
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86"
+IUSE=""
+
+RDEPEND="!<sci-biology/emboss-6.0.1
+ !sci-biology/embassy-meme
+ !sci-biology/embassy-phylip
+ ~sci-biology/emboss-6.0.1
+ =sci-biology/embassy-cbstools-1.0.0
+ =sci-biology/embassy-domainatrix-0.1.0-r3
+ =sci-biology/embassy-domalign-0.1.0-r3
+ =sci-biology/embassy-domsearch-0.1.0-r3
+ =sci-biology/embassy-emnu-1.05-r5
+ =sci-biology/embassy-esim4-1.0.0-r5
+ =sci-biology/embassy-hmmer-2.3.2-r2
+ =sci-biology/embassy-iprscan-4.3.1
+ =sci-biology/embassy-memenew-0.1.0-r1
+ =sci-biology/embassy-mira-2.8.2
+ =sci-biology/embassy-mse-1.0.0-r6
+ =sci-biology/embassy-phylipnew-3.67
+ =sci-biology/embassy-signature-0.1.0-r3
+ =sci-biology/embassy-structure-0.1.0-r3
+ =sci-biology/embassy-topo-1.0.0-r5
+ =sci-biology/embassy-vienna-1.7.2"
diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild
new file mode 100644
index 000000000000..d663e22efda3
--- /dev/null
+++ b/sci-biology/embassy/embassy-6.6.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
+HOMEPAGE="http://emboss.sourceforge.net/embassy/"
+
+LICENSE+=" freedist"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+="
+ >=sci-biology/embassy-cbstools-1.0.0.650
+ >=sci-biology/embassy-clustalomega-1.1.0
+ >=sci-biology/embassy-domainatrix-0.1.650
+ >=sci-biology/embassy-domalign-0.1.650
+ >=sci-biology/embassy-domsearch-0.1.650
+ >=sci-biology/embassy-emnu-1.05.650
+ >=sci-biology/embassy-esim4-1.0.0.650
+ >=sci-biology/embassy-hmmer-2.3.2.650
+ >=sci-biology/embassy-iprscan-4.3.1.650
+ >=sci-biology/embassy-meme-4.7.650
+ >=sci-biology/embassy-mse-3.0.0.650
+ >=sci-biology/embassy-phylipnew-3.69.650
+ >=sci-biology/embassy-signature-0.1.650
+ >=sci-biology/embassy-structure-0.1.650
+ >=sci-biology/embassy-topo-2.0.650
+ >=sci-biology/embassy-vienna-1.7.2.650
+"
diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
new file mode 100644
index 000000000000..c364f2c77e86
--- /dev/null
+++ b/sci-biology/emboss/Manifest
@@ -0,0 +1,4 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
+DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
+DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c
diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
new file mode 100644
index 000000000000..0edfd7a639d0
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.0.1.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=1
+
+inherit eutils
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE="X png minimal"
+
+DEPEND="
+ X? ( x11-libs/libXt )
+ png? (
+ sys-libs/zlib
+ media-libs/libpng
+ media-libs/gd
+ )
+ !minimal? (
+ sci-biology/primer3
+ sci-biology/clustalw
+ )"
+
+RDEPEND="${DEPEND}
+ !sys-devel/cons"
+
+PDEPEND="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ sci-biology/transfac
+ )"
+
+S="${WORKDIR}/EMBOSS-${PV}"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
+
+ local link_string="$(pkg-config --libs x11)"
+ if use png; then
+ link_string="${link_string} -lgd $(pkg-config --libs libpng)"
+ fi
+ sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
+ || die "Failed to patch ajax Makefile"
+}
+
+src_compile() {
+ local myconf
+ myconf="--includedir=${D}/usr/include/emboss"
+ use X || myconf="${EXTRA_CONF} --without-x"
+ use png || myconf="${EXTRA_CONF} --without-pngdriver"
+
+ econf ${myconf}
+ # Do not install the JEMBOSS component (the --without-java configure option
+ # does not work). JEMBOSS will eventually be available as a separate package.
+ sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
+ Makefile || die
+ emake || die
+}
+
+src_install() {
+ einstall || die "Failed to install program files."
+
+ dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
+ || die "Failed to install documentation."
+ newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
+ || die "Failed to install Gentoo readme file."
+
+ # Install env file for setting libplplot and acd files path.
+ cat <<- EOF > 22emboss
+ # plplot libs dir
+ PLPLOT_LIB="/usr/share/EMBOSS/"
+ # ACD files location
+ EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
+ EOF
+ doenvd 22emboss || die "Failed to install environment file."
+
+ # Symlink preinstalled docs to "/usr/share/doc".
+ dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
+ dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
+ dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
+ dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
+
+ # Clashes #330507
+ mv "${D}"/usr/bin/{digest,pepdigest} || die
+
+ # Remove useless dummy files from the image.
+ find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+ # Move the provided codon files to a different directory. This will avoid
+ # user confusion and file collisions on case-insensitive file systems (see
+ # bug #115446). This change is documented in "README.Gentoo".
+ mv "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+ die "Failed to move CODON directory."
+
+ # Move the provided restriction enzyme prototypes file to a different name.
+ # This avoids file collisions with versions of rebase that install their
+ # own enzyme prototypes file (see bug #118832).
+ mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+ die "Failed to move enzyme equivalence file."
+}
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
new file mode 100644
index 000000000000..e8baba4c7752
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit autotools eutils
+
+MY_PATCH="4"
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="
+ ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
+ ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
+
+LICENSE="GPL-2 LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc minimal mysql pdf png postgres static-libs X"
+
+DEPEND="
+ dev-libs/expat
+ dev-libs/libpcre:3
+ sci-libs/plplot
+ sys-libs/zlib
+ mysql? ( virtual/mysql )
+ pdf? ( media-libs/libharu )
+ png? (
+ sys-libs/zlib
+ media-libs/libpng
+ media-libs/gd
+ )
+ postgres? ( dev-db/postgresql )
+ !minimal? (
+ sci-biology/primer3
+ sci-biology/clustalw
+ )
+ X? ( x11-libs/libXt )"
+RDEPEND="${DEPEND}
+ !sys-devel/cons"
+PDEPEND="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ sci-biology/transfac
+ )"
+
+S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
+
+src_prepare() {
+ epatch "${WORKDIR}"/${P}.patch
+ epatch \
+ "${FILESDIR}"/${PV}-unbundle-libs.patch \
+ "${FILESDIR}/${PF}_plcol.patch"
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_with X x) \
+ $(use_with png pngdriver "${EPREFIX}/usr") \
+ $(use_with doc docroot "${EPREFIX}/usr") \
+ $(use_with pdf hpdf "${EPREFIX}/usr") \
+ $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
+ $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
+ $(use_enable amd64 64) \
+ $(use_enable static-libs static) \
+ --without-java \
+ --enable-large \
+ --enable-systemlibs \
+ --includedir="${ED}/usr/include/emboss"
+}
+
+src_install() {
+ einstall || die "Failed to install program files."
+
+ dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+ sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
+ dodoc README.Gentoo
+
+ # Install env file for setting libplplot and acd files path.
+ cat <<- EOF > 22emboss
+ # plplot libs dir
+ PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
+ # ACD files location
+ EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+ EOF
+ doenvd 22emboss
+
+ # Symlink preinstalled docs to "/usr/share/doc".
+ dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+ dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+ dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+ dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
+
+ # Clashes #330507
+ mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
+ # Remove useless dummy files from the image.
+ find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+ # Move the provided codon files to a different directory. This will avoid
+ # user confusion and file collisions on case-insensitive file systems (see
+ # bug #115446). This change is documented in "README.Gentoo".
+ mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+ die "Failed to move CODON directory."
+
+ # Move the provided restriction enzyme prototypes file to a different name.
+ # This avoids file collisions with versions of rebase that install their
+ # own enzyme prototypes file (see bug #118832).
+ mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+ die "Failed to move enzyme equivalence file."
+}
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
new file mode 100644
index 000000000000..22d650f1107a
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+inherit autotools-utils emboss-r1 eutils readme.gentoo
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE+=" minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
+
+RDEPEND+=" !sys-devel/cons"
+PDEPEND+="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/primer3
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ )"
+
+S="${WORKDIR}"/EMBOSS-${PV}
+
+DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )
+
+PATCHES=(
+ "${FILESDIR}"/${P}_fix-build-system.patch
+ "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+ "${FILESDIR}"/${P}_plplot-declarations.patch
+ "${FILESDIR}"/${P}_qa-implicit-declarations.patch
+)
+
+src_install() {
+ # Use autotools-utils_* to remove useless *.la files
+ autotools-utils_src_install
+
+ readme.gentoo_create_doc
+
+ # Install env file for setting libplplot and acd files path.
+ cat > 22emboss <<- EOF
+ # ACD files location
+ EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+ EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
+ EOF
+ doenvd 22emboss
+
+ # Remove useless dummy files
+ find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."
+
+ # Move the provided codon files to a different directory. This will avoid
+ # user confusion and file collisions on case-insensitive file systems (see
+ # bug #115446). This change is documented in "README.gentoo".
+ mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+ die "Failed to move CODON directory."
+}
diff --git a/sci-biology/emboss/files/22emboss b/sci-biology/emboss/files/22emboss
new file mode 100644
index 000000000000..177643ced11f
--- /dev/null
+++ b/sci-biology/emboss/files/22emboss
@@ -0,0 +1,4 @@
+# plplot libs dir
+PLPLOT_LIB="/usr/share/EMBOSS/"
+# ACD files location
+EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
diff --git a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch
new file mode 100644
index 000000000000..5e463744a739
--- /dev/null
+++ b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch
@@ -0,0 +1,600 @@
+diff --git a/Makefile.am b/Makefile.am
+index 4fe2ed1..7f3a95f 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4
+
+ AUTOMAKE_OPTIONS = gnits
+
+-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
++if !ESYSTEMLIBS
++EXTRA_DIRS = plplot
++endif
++
++if GJEMBOSS
++JEMBOSS_DIR = jemboss
++endif
++
++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
+
+ # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
+
+ # files with nonstandard names in this directory
+-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
+
+ # tar to pick up the other directories
+ # then remove any CVS subdirectories
+diff --git a/README.fixes b/README.fixes
+new file mode 100644
+index 0000000..3c56d79
+--- /dev/null
++++ b/README.fixes
+@@ -0,0 +1,9 @@
++The files in this directory are bugfix replacements for files in
++the EMBOSS-6.3.1 distribution. Just drop the replacement files in
++the location shown and redo the 'make install.'
++
++Fix 1. EMBOSS-6.3.1/configure
++ EMBOSS-6.3.1/m4/mysql.m4
++
++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
++ hpdf support prevented inclusion of MySQL support.
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index 4a44f6f..cf27ff8 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,6 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
+ if !ESYSTEMLIBS
+-EXTRA_DIRS = expat zlib
++EXTRA_DIRS = pcre expat zlib
+ endif
+
+-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 02bcaa7..368ddfe 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core \
+ -I$(top_srcdir)/ajax/graphics \
+@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libacd_la_LDFLAGS = $(LINKFLAGS)
++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index da57727..857ca5f 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
+
+@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajaxdb_la_LDFLAGS = $(LINKFLAGS)
++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index af27cb0..8fa4a3a 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_LIBS = -lexpat -lpcre
+ endif
+
++EXTRA_DIST = ajax-pcre-config.h.in
++DISTCLEAN = ajax-pcre-config.h
+
+ INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
+ -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
+--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
+
+ AJAXSRC = ajalign.c ajarr.c ajassert.c \
+ ajbase.c ajcall.c ajcod.c \
+@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \
+ ajmath.h ajmatrices.h ajmem.h ajmess.h \
+ ajnam.h ajnexus.h ajobo.h \
+ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
+-ajrange.h ajreg.h ajreport.h ajresource.h \
++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
+ ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \
+ ajsort.h ajsql.h ajstr.h ajsys.h \
+ ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
+@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajax_la_LDFLAGS = $(LINKFLAGS)
++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
+diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
+new file mode 100644
+index 0000000..b09e4e6
+--- /dev/null
++++ b/ajax/core/ajax-pcre-config.h.in
+@@ -0,0 +1 @@
++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 06793be..659f462 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -16,9 +16,14 @@ extern "C"
+ #define ajreg_h
+
+ #include "ajax.h"
++#include "ajax-pcre-config.h"
++#ifndef AJAX_USE_SYSTEM_PCRE
+ #include "pcre_config.h"
+ #include "pcre_internal.h"
+ #include "pcreposix.h"
++#else
++#include <pcre.h>
++#endif
+
+ #define AJREG_OVECSIZE 30
+
+@@ -41,7 +46,11 @@ extern "C"
+ ******************************************************************************/
+
+ typedef struct AjSRegexp {
++#ifndef AJAX_USE_SYSTEM_PCRE
+ real_pcre *pcre;
++#else
++ pcre *pcre;
++#endif
+ pcre_extra *extra;
+ int *ovector;
+ const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index ca33a84..87e51bd 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
+--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
++INCLUDES = $(EXTRA_INCLUDES) \
++-I$(top_srcdir)/ajax/core
+
+ ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
+ ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
+@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libensembl_la_LDFLAGS = $(LINKFLAGS)
++libensembl_la_LIBADD = ../core/libajax.la
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index ab45afc..f61c605 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot
+ endif
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
++EXTRA_LIBS = $(PLPLOT_LIBS)
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
+
+ AJAXGSRC = ajgraph.c ajhist.c
+@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libajaxg_la_LDFLAGS = $(LINKFLAGS)
++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
+diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
+index 25e75e4..60f2743 100644
+--- a/ajax/graphics/ajgraph.c
++++ b/ajax/graphics/ajgraph.c
+@@ -34,10 +34,8 @@
+ #include <float.h>
+ #define AZ 28
+
+-
+ #include "plplotP.h"
+
+-
+ static void GraphArray(ajuint numofpoints,
+ float *x, float *y);
+ static void GraphArrayGaps(ajuint numofpoints,
+@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
+ ** @@
+ ******************************************************************************/
+
++#define _GNU_SOURCE
++#include <stdio.h>
++
+ static void GraphSetName(const AjPGraph thys,
+ const AjPStr txt, const char *ext)
+ {
+ if(!thys->ready)
+ {
++#ifdef USE_PLXSFNAM_SHIM
++ char *fullname;
++#endif
+ ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
++#ifdef USE_PLXSFNAM_SHIM
++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
++ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
++ plsfnam(fullname);
++ free(fullname);
++#else
+ plxsfnam(ajStrGetPtr(txt), ext);
++#endif
+ ajStrAssignS(&graphBasename, txt);
+ ajStrAssignC(&graphExtension, ext);
+ if(ajStrGetCharFirst(graphExtension) == '.')
+diff --git a/configure.in b/configure.in
+index ddb4f81..3f4fe5e 100644
+--- a/configure.in
++++ b/configure.in
+@@ -235,15 +235,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" != "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+
+ # Checks for header files.
+ #as# AC_PATH_X
+@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove)
+ #as# select socket sqrt strchr strcspn strdup strerror strpbrk \
+ #as# strrchr strspn strstr strtol])
+
+-if test "${with_x}" != "no" ; then
+-LF_EMBOSS_PATH_XLIB
+-fi
+
+ dnl Library checks
+ AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
+@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
+ CHECK_AUTH
+ CHECK_AMD64
+
++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes")
++
+ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+
+
+ dnl Check for 'ant' for packaging Jemboss and export result
+@@ -443,13 +433,36 @@ fi
+
+ dnl Test if --enable-systemlibs given
+ have_systemlibs=no
++DEFINE_USE_SYSTEM_PCRE="#undef"
+ AC_ARG_ENABLE(systemlibs,
+ AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
++AC_MSG_CHECKING(for systemlib usage)
+ if test "${enable_systemlibs}" = "yes" ; then
+ have_systemlibs=yes
++ DEFINE_USE_SYSTEM_PCRE="#define"
++ PKG_CHECK_MODULES([PLPLOT], [plplotd])
++ PKG_CHECK_MODULES([ZLIB], [zlib])
++else
++ dnl X11 is only used by plplot
++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
++ if test "${with_x}" != "no" ; then
++ if test "`uname -a | grep Darwin`"; then
++ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++ if test ${OSXX} '>' '10.4'; then
++ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++ fi
++ fi
++ fi
++ if test "${with_x}" != "no" ; then
++ LF_EMBOSS_PATH_XLIB
++ fi
++ AC_MSG_NOTICE(USING bundled LIBS)
+ fi
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+
+
+
+@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
+
+ dnl Test if purify exists and if --enable-purify given if so
+ dnl set "-g"
+-
+ AC_MSG_CHECKING(for purify)
+ dnl if(purify -version) < /dev/null > /dev/null 2>&1; then
+ AC_ARG_ENABLE(purify,
+@@ -683,6 +695,7 @@ CHECK_THREADS
+
+
+ AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
++ajax/core/ajax-pcre-config.h
+ ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
+ ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
+ ajax/acd/Makefile
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 0820517..a0257b2 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \
+ yank
+
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+
+-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
++INCLUDES = -I$(top_srcdir)/nucleus \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
++ -I$(top_srcdir)/ajax/acd
+
+
+ aaindexextract_SOURCES = aaindexextract.c
+@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c
+ treetypedisplay_SOURCES = treetypedisplay.c
+
+ if !ESYSTEMLIBS
+-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la
+ endif
+
+
+@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
+ ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
+ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
+ $(EXTRA_LDS) \
+- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
+ $(XLIB)
+
+ pkgdata_DATA = emboss.default.template
+diff --git a/m4/mysql.m4 b/m4/mysql.m4
+index fe413af..ebea25c 100644
+--- a/m4/mysql.m4
++++ b/m4/mysql.m4
+@@ -1,4 +1,6 @@
+-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
++# ===========================================================================
++# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
++# ===========================================================================
+ #
+ # SYNOPSIS
+ #
+@@ -6,19 +8,18 @@
+ #
+ # DESCRIPTION
+ #
+-# This macro provides tests of availability of MySQL client library
+-# of particular version or newer.
++# This macro provides tests of availability of MySQL client library of
++# particular version or newer.
+ #
+-# AX_LIB_MYSQL macro takes only one argument which is optional. If
+-# there is no required version passed, then macro does not run
+-# version test.
++# AX_LIB_MYSQL macro takes only one argument which is optional. If there
++# is no required version passed, then macro does not run version test.
+ #
+ # The --with-mysql option takes one of three possible values:
+ #
+ # no - do not check for MySQL client library
+ #
+-# yes - do check for MySQL library in standard locations
+-# (mysql_config should be in the PATH)
++# yes - do check for MySQL library in standard locations (mysql_config
++# should be in the PATH)
+ #
+ # path - complete path to mysql_config utility, use this option if
+ # mysql_config can't be found in the PATH
+@@ -33,27 +34,23 @@
+ #
+ # HAVE_MYSQL
+ #
+-# LAST MODIFICATION
++# LICENSE
+ #
+-# 2006-07-16
+-# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers,
+-# which prevents gdb from displaying stack traces.
+-# Changed mysql_config --cflags to mysql_config --include
++# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
+ #
+-# COPYLEFT
+-#
+-# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
+-#
+-# Copying and distribution of this file, with or without
+-# modification, are permitted in any medium without royalty provided
+-# the copyright notice and this notice are preserved.
++# Copying and distribution of this file, with or without modification, are
++# permitted in any medium without royalty provided the copyright notice
++# and this notice are preserved. This file is offered as-is, without any
++# warranty.
++
++#serial 12
+
+ AC_DEFUN([AX_LIB_MYSQL],
+ [
+ AC_ARG_WITH([mysql],
+- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
++ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
+ [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
+- )],
++ ),
+ [
+ if test "$withval" = "no"; then
+ want_mysql="no"
+@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
+ ],
+ [want_mysql="yes"]
+ )
++ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
+
+ MYSQL_CFLAGS=""
+ MYSQL_LDFLAGS=""
+ MYSQL_VERSION=""
+
+ dnl
+- dnl Check MySQL libraries (libpq)
++ dnl Check MySQL libraries
+ dnl
+
+ if test "$want_mysql" = "yes"; then
+
+- if test -z "$MYSQL_CONFIG" -o test; then
+- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
++ if test -z "$MYSQL_CONFIG" ; then
++ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
+ fi
+
+ if test "$MYSQL_CONFIG" != "no"; then
+@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+
+ MYSQL_VERSION=`$MYSQL_CONFIG --version`
+
+-dnl It isn't enough to just test for mysql_config as Fedora
+-dnl provides it in the mysql RPM even though mysql-devel may
+-dnl not be installed
+-
+- EMBCFLAGS=$CFLAGS
+- EMBLDFLAGS=$LDFLAGS
+- CFLAGS=$MYSQL_CFLAGS
+- LDFLAGS=$MYSQL_LDFLAGS
+-
+- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+- #include "mysql.h"]],
+- [[mysql_info(NULL)]])],
+- [havemysql=yes],
+- [havemysql=no])
+-
+- CFLAGS=$EMBCFLAGS
+- LDFLAGS=$EMBLDFLAGS
+-
+- if test "$havemysql" = yes; then
+- AC_DEFINE([HAVE_MYSQL], [1],
+- [Define to 1 if MySQL libraries are available])
+- found_mysql="yes"
+- AC_MSG_RESULT([yes])
+- else
+- MYSQL_CFLAGS=""
+- MYSQL_LDFLAGS=""
+- found_mysql="no"
+- AC_MSG_RESULT([no])
+- fi
++ found_mysql="yes"
++ AC_MSG_RESULT([yes])
+ else
+ found_mysql="no"
+ AC_MSG_RESULT([no])
+@@ -170,6 +141,11 @@ dnl not be installed
+ fi
+ fi
+
++ if test "$found_mysql" = "yes" ; then
++ AC_DEFINE([HAVE_MYSQL], [1],
++ [Define to 1 if MySQL libraries are available])
++ fi
++
+ AC_SUBST([MYSQL_VERSION])
+ AC_SUBST([MYSQL_CFLAGS])
+ AC_SUBST([MYSQL_LDFLAGS])
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index c244786..ff301b9 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
+@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \
+ -lezlib -leplplot
+ else
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+ endif
+
+
+-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
+- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
++INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
++ -I$(top_srcdir)/ajax \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+
+ libnucleus_la_LDFLAGS = $(LINKFLAGS)
++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
diff --git a/sci-biology/emboss/files/README.Gentoo b/sci-biology/emboss/files/README.Gentoo
new file mode 100644
index 000000000000..ce37576f0fc4
--- /dev/null
+++ b/sci-biology/emboss/files/README.Gentoo
@@ -0,0 +1,28 @@
+Using EMBOSS on Gentoo systems
+
+Codon data files location
+
+The codon data files that are distributed with EMBOSS are installed in the
+"/usr/share/EMBOSS/data/CODONS.orig" directory instead of the usual
+"/usr/share/EMBOSS/data/CODONS". This is done to avoid confusion between these
+codon files and those installed with the CUTG database. The names of these files
+sometimes vary only by their case. Having both sets of files in the same directory
+is also impossible on systems such as MacOSX, where the root filesystem is case
+insensitive. If you do not have the CUTG database installed and want to use the
+codon files distributed with EMBOSS, you can symlink the "CODONS.orig" directory
+to "CODONS":
+
+ cd /usr/share/EMBOSS/data
+ ln -s CODONS.orig CODONS
+
+Restriction enzymes equivalence file location
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed as
+"/usr/share/EMBOSS/data/embossre.equ.orig" rather than the usual
+"/usr/share/EMBOSS/data/embossre.equ". This is done to avoid a file collision
+with the equivalence file provided by the Rebase database. If you do not have the
+Rebase database installed and want to use the equivalence file distributed with
+EMBOSS, you can symlink the "embossre.equ.orig" file to "embossre.equ":
+
+ cd /usr/share/EMBOSS/data
+ ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo
new file mode 100644
index 000000000000..d1879bd0811c
--- /dev/null
+++ b/sci-biology/emboss/files/README.gentoo
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+ # cd ${EPREFIX}/usr/share/EMBOSS/data
+ # ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+ # cd ${EPREFIX}/usr/share/EMBOSS/data
+ # ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch
new file mode 100644
index 000000000000..9915f95376d0
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch
@@ -0,0 +1,24 @@
+diff -Naur EMBOSS-5.0.0.old/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in
+--- EMBOSS-5.0.0.old/ajax/Makefile.in 2007-07-12 05:53:32.000000000 -0500
++++ EMBOSS-5.0.0/ajax/Makefile.in 2008-01-25 16:43:51.000000000 -0500
+@@ -244,7 +244,7 @@
+ top_srcdir = @top_srcdir@
+ @ISCYGWIN_FALSE@lib_LTLIBRARIES = libajax.la libajaxg.la
+ @ISCYGWIN_TRUE@lib_LTLIBRARIES = libajax.la
+-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -lm -L../plplot/.libs -leplplot
+ @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
+ @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
+ @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
+diff -Naur EMBOSS-5.0.0.old/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in
+--- EMBOSS-5.0.0.old/plplot/Makefile.in 2007-07-12 05:53:36.000000000 -0500
++++ EMBOSS-5.0.0/plplot/Makefile.in 2008-01-25 16:42:51.000000000 -0500
+@@ -229,7 +229,7 @@
+ lib_LTLIBRARIES = libeplplot.la
+ @AMPNG_FALSE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lX11
+ @AMPNG_TRUE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lgd -lpng -lz -lX11 -lm
+-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = PATCH_PLPLOT
+ @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -lX11 -lgd -lpng -lz
+ INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\"
+ PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
new file mode 100644
index 000000000000..0f5e592b77f1
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
@@ -0,0 +1,112 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200
++++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1645,14 +1645,14 @@
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+
+ static void GraphSetPen(ajint colour)
+ {
+- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
+- plcol((PLINT)colour);
++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
++ plcol0((PLINT)colour);
+
+ return;
+ }
+
+
+
+--- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200
++++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200
+@@ -1709,13 +1709,13 @@
+ if (plsc->zdigmax == 0)
+ plsc->zdigmax = 3;
+
+ /* Switch to graphics mode and set color and arrow style*/
+
+ plgra();
+- plcol(1);
++ plcol0(1);
+
+ plstyl(0, &mk, &sp);
+ plpat(1, &inc, &del);
+
+ plsvect(def_arrow_x, def_arrow_y, 6, 0);
+
+--- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200
++++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200
+@@ -153,17 +153,17 @@
+
+ plgchr(&sc, &dy);
+ sc = dy = dy/100;
+ plwind(-0.01, 1.01, -0.01, 1.01);
+ for (i=0; i<PEN; i++) {
+ if (mystripc->npts[i] || first) {
+- plcol(mystripc->colline[i]);
++ plcol0(mystripc->colline[i]);
+ pllsty(mystripc->styline[i]);
+ pljoin(mystripc->xlpos, mystripc->ylpos - sc,
+ mystripc->xlpos + 0.1, mystripc->ylpos - sc);
+- plcol(mystripc->collab);
++ plcol0(mystripc->collab);
+ plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
+ 0., 0., 0, mystripc->legline[i]);
+ sc += dy;
+ }
+ }
+ plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
+@@ -184,34 +184,34 @@
+ PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
+
+ /* Set up window */
+
+ plvpor(0,1,0,1);
+ plwind(0,1,0,1);
+- plcol(0);plpsty(0);
++ plcol0(0);plpsty(0);
+ plfill(4, &x[0], &y[0]);
+ plvsta();
+
+ /* Draw box and same window dimensions */
+ mystrip->wxmin=mystrip->xmin;
+ mystrip->wxmax=mystrip->xmax;
+ mystrip->wymin=mystrip->ymin;
+ mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
+
+ plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
+
+ pllsty(1);
+- plcol(mystrip->colbox);
++ plcol0(mystrip->colbox);
+ plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
+
+- plcol(mystrip->collab);
++ plcol0(mystrip->collab);
+ pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
+
+ for (i=0; i<PEN; i++) {
+ if (mystrip->npts[i] > 0) {
+- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
++ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
+ plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
+ }
+ }
+
+ plstrip_legend(mystrip,0);
+ }
+@@ -269,13 +269,13 @@
+ if (stripc->xmax - stripc->xmin < stripc->xlen) {
+ if( yasc == 0) {
+
+ /* If user has changed subwindow, make shure we have the correct one */
+ plvsta();
+ plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
+- plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
++ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
+ if ((stripc->npts[p]-2) < 0)
+ plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ else
+ plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
+ plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ plflush();
diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
new file mode 100644
index 000000000000..7704873e9d26
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
@@ -0,0 +1,11 @@
+--- EMBOSS-6.6.0/emboss/embossversion.c
++++ EMBOSS-6.6.0/emboss/embossversion.c
+@@ -415,7 +415,7 @@
+ ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING);
+ #endif
+ #ifdef _FORTIFY_SOURCE
+- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE);
++ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL);
+ #endif
+ ajFmtPrintF(outfile, "\n");
+ ajFmtPrintF(outfile, "Sizes (bytes):\n");
diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
new file mode 100644
index 000000000000..266bddd95a37
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
@@ -0,0 +1,411 @@
+ Makefile.am | 9 +++---
+ ajax/Makefile.am | 4 +--
+ ajax/acd/Makefile.am | 8 +++--
+ ajax/ajaxdb/Makefile.am | 6 ++--
+ ajax/core/Makefile.am | 6 ++--
+ ajax/core/ajreg.h | 7 ++--
+ ajax/ensembl/Makefile.am | 6 ++--
+ ajax/graphics/Makefile.am | 8 +++--
+ configure.ac | 82 ++++++++++++++++++++++++++---------------------
+ emboss/Makefile.am | 13 +++++---
+ jemboss/lib/Makefile.am | 2 +-
+ m4/idxdbs.m4 | 17 +++-------
+ nucleus/Makefile.am | 8 +++--
+ 13 files changed, 100 insertions(+), 76 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 177dec5..18dd99a 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -12,8 +12,11 @@ LICENSE \
+ ONEWS \
+ PROBLEMS
+
+-SUBDIRS = \
+-plplot \
++SUBDIRS =
++if !ESYSTEMLIBS
++SUBDIRS += plplot
++endif
++SUBDIRS += \
+ ajax \
+ nucleus \
+ emboss \
+@@ -33,5 +36,3 @@ dist-hook:
+ tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
+ tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
+
+-install-exec-hook:
+- $(bindir)/embossupdate
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index f27472c..de34e17 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,7 +1,7 @@
+ ## Process this file with automake to produce Makefile.in
+
+-SUBDIRS = pcre
++SUBDIRS =
+ if !ESYSTEMLIBS
+-SUBDIRS += expat zlib
++SUBDIRS += pcre expat zlib
+ endif
+ SUBDIRS += core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 9f0f700..3295a1d 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -3,16 +3,20 @@
+ lib_LTLIBRARIES = libacd.la
+
+ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
+
+ libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb
++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ if !ESYSTEMLIBS
++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++libacd_la_CFLAGS += $(PLPLOT_CFLAGS)
++endif
+ libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+
+ libacd_la_LDFLAGS = -version-info 6:5:0
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index c2b0c00..9de14fe 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -3,14 +3,16 @@
+ lib_LTLIBRARIES = libajaxdb.la
+
+ libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
+
+ libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl
+-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
+ libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index 2906837..3189c34 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -3,13 +3,15 @@
+ lib_LTLIBRARIES = libajax.la
+
+ libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
+
+-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
++libajax_la_CPPFLAGS =
+ if !ESYSTEMLIBS
++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 1623c82..5d928cf 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -39,9 +39,8 @@
+ #include "ajdefine.h"
+ #include "ajstr.h"
+
+-#include "pcre_config.h"
+-#include "pcre_internal.h"
+-#include "pcreposix.h"
++#include <pcre.h>
++#include <pcreposix.h>
+
+ AJ_BEGIN_DECLS
+
+@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
+
+ typedef struct AjSRegexp
+ {
+- real_pcre *pcre;
++ struct real_pcre *pcre;
+ pcre_extra *extra;
+ int *ovector;
+ const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index 0d1250b..5484c02 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -3,13 +3,15 @@
+ lib_LTLIBRARIES = libensembl.la
+
+ libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libensembl_la_LIBADD = ../core/libajax.la
+
+-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
++libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+
+ libensembl_la_LDFLAGS = -version-info 6:5:0
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index a4f202b..1114c2c 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -3,12 +3,16 @@
+ lib_LTLIBRARIES = libajaxg.la
+
+ libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS)
+
+-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
++libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+-endif
+ libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS)
++endif
+ libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+
+ libajaxg_la_LDFLAGS = -version-info 6:5:0
+diff --git a/configure.ac b/configure.ac
+index a7bd9c6..9ba3121 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -629,32 +629,6 @@ AS_CASE([${host_os}],
+
+
+
+-
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+ dnl Define where the EMBOSS package is located
+ AC_SUBST([AJAX_FIXED_ROOT])
+ AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
+@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL
+
+
+
+-dnl "Export" these variables for PCRE
+
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+
+
+
+@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs],
+
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++ PKG_CHECK_MODULES([PCRE], [libpcre])
++ PKG_CHECK_MODULES([EXPAT], [expat])
++ PKG_CHECK_MODULES([ZLIB], [zlib])
++ PKG_CHECK_MODULES([PLPLOT], [plplotd],
++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++ )
++],
++[
++dnl using bundled libraries
++ dnl PCRE library definitions - see the MAJOR and MINOR values
++ dnl to see which version's configure.ac these lines come from
+
++ dnl Provide the current PCRE version information. Do not use numbers
++ dnl with leading zeros for the minor version, as they end up in a C
++ dnl macro, and may be treated as octal constants. Stick to single
++ dnl digits for minor numbers less than 10. There are unlikely to be
++ dnl that many releases anyway.
++
++ PCRE_MAJOR="7"
++ PCRE_MINOR="9"
++ PCRE_DATE="11-Apr-2009"
++ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
++
++ dnl Default values for miscellaneous macros
++
++ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
++
++ dnl Provide versioning information for libtool shared libraries that
++ dnl are built by default on Unix systems.
++
++ PCRE_LIB_VERSION="0:1:0"
++ PCRE_POSIXLIB_VERSION="0:0:0"
++
++ dnl "Export" these variables for PCRE
++ AC_SUBST([HAVE_MEMMOVE])
++ AC_SUBST([HAVE_STRERROR])
++ AC_SUBST([PCRE_MAJOR])
++ AC_SUBST([PCRE_MINOR])
++ AC_SUBST([PCRE_DATE])
++ AC_SUBST([PCRE_VERSION])
++ AC_SUBST([PCRE_LIB_VERSION])
++ AC_SUBST([PCRE_POSIXLIB_VERSION])
++ AC_SUBST([POSIX_MALLOC_THRESHOLD])
++])
+
+
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 89ada78..f987d40 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -28,15 +28,18 @@ endif
+
+ AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
++if !ESYSTEMLIBS
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+-if !ESYSTEMLIBS
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+-AM_CPPFLAGS += -I$(top_srcdir)/nucleus
+ AM_CPPFLAGS += -I$(top_srcdir)/plplot
++else
++AM_CFLAGS += $(PLPLOT_CFLAGS)
++endif
++AM_CPPFLAGS += -I$(top_srcdir)/nucleus
+ AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
+ AM_CPPFLAGS += $(JAVA_CPPFLAGS)
+
+@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
+ if !ESYSTEMLIBS
+ LDADD += ../ajax/zlib/libezlib.la
+ LDADD += ../ajax/expat/libeexpat.la
+-endif
+ LDADD += ../ajax/pcre/libepcre.la
+ LDADD += ../plplot/libeplplot.la
++else
++LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS)
++endif
+ LDADD += $(XLIB)
+
+ #if PURIFY
+diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
+index 5f7e21e..8b45ce2 100644
+--- a/jemboss/lib/Makefile.am
++++ b/jemboss/lib/Makefile.am
+@@ -12,7 +12,7 @@ mail.jar \
+ jalviewApplet.jar \
+ jemboss.jar
+
+-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
+ if JAVA_BUILD
+ $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
+ endif
+diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
+index 0ca7ea9..9b54f2a 100644
+--- a/m4/idxdbs.m4
++++ b/m4/idxdbs.m4
+@@ -1,17 +1,8 @@
+ AC_DEFUN([CHECK_IDXDBS],
+ [
+-AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
+
+-
+-if test -f ./emboss/index/edam.xac; then
+-AC_MSG_RESULT(yes)
+-else
+-AC_MSG_RESULT(no)
+-echo ""
+-echo "Pre-indexed edam, taxon + drcat databases not found."
+-echo "Please download them from within this directory using:"
+-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
+-echo "and then repeat the configure step."
+-exit 1
+-fi
++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
++ [],
++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
+ ])
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index 37b8543..5819c89 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
+@@ -3,6 +3,7 @@
+ lib_LTLIBRARIES = libnucleus.la
+
+ libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
+
+ if ISSHARED
+ if ISAIXIA64
+@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
+ endif
+ endif
+
+-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot
+-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
+ if !ESYSTEMLIBS
++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
++else
++libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS)
+ endif
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
+ libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
new file mode 100644
index 000000000000..15f5f967a07d
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
@@ -0,0 +1,61 @@
+--- EMBOSS-6.6.0/ajax/graphics/ajgraph.c
++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c
+@@ -49,7 +49,7 @@
+
+ #define GRAPH_DEBUG 1
+
+-#include "plplotP.h"
++#include <plplotP.h>
+
+
+ static void GraphArray(ajuint numofpoints,
+@@ -964,10 +964,10 @@
+ if(!thys->ready)
+ {
+ #if GRAPH_DEBUG
+- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
++ ajDebug("=g= plsfnam ('%S')\n", txt);
+ #endif
+
+- plxsfnam(ajStrGetPtr(txt), ext);
++ plsfnam(ajStrGetPtr(txt));
+ ajStrAssignS(&graphBasename, txt);
+ ajStrAssignC(&graphExtension, ext);
+ if(ajStrGetCharFirst(graphExtension) == '.')
+@@ -1213,10 +1213,10 @@
+ void ajGraphicsSetPenwidth(float penwidth)
+ {
+ #if GRAPH_DEBUG
+- ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
++ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth);
+ #endif
+
+- plwid((PLINT)penwidth);
++ c_plwidth((PLINT)penwidth);
+
+ return;
+ }
+@@ -1538,10 +1538,10 @@
+ static void GraphSetPen(ajint colour)
+ {
+ #if GRAPH_DEBUG
+- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
+ #endif
+
+- plcol((PLINT)colour);
++ plcol0((PLINT)colour);
+
+ return;
+ }
+--- EMBOSS-6.6.0/ajax/graphics/ajgraph.h
++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h
+@@ -32,7 +32,7 @@
+ /* ========================================================================= */
+
+ #include "ajdefine.h"
+-#include "plplot.h"
++#include <plplot.h>
+ #include "ajgraphstruct.h"
+ #include "ajdefine.h"
+ #include "ajstr.h"
diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
new file mode 100644
index 000000000000..eff10b2e6700
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
@@ -0,0 +1,74 @@
+--- EMBOSS-6.6.0/ajax/core/ajfeatread.c
++++ EMBOSS-6.6.0/ajax/core/ajfeatread.c
+@@ -45,6 +45,7 @@
+
+ #include <limits.h>
+ #include <math.h>
++#include <string.h>
+ #include <errno.h>
+
+ #ifdef WIN32
+--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
++++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
+@@ -43,7 +43,7 @@
+
+ #include <limits.h>
+ #include <math.h>
+-
++#include <string.h>
+
+ static AjPRegexp featoutRegUfoFmt = NULL;
+ static AjPRegexp featoutRegUfoFile = NULL;
+--- EMBOSS-6.6.0/ajax/core/ajpdbio.c
++++ EMBOSS-6.6.0/ajax/core/ajpdbio.c
+@@ -37,7 +37,7 @@
+
+ #include <limits.h>
+ #include <math.h>
+-
++#include <string.h>
+
+
+
+--- EMBOSS-6.6.0/ajax/core/ajreg.c
++++ EMBOSS-6.6.0/ajax/core/ajreg.c
+@@ -32,6 +32,7 @@
+ #include "ajlib.h"
+
+ #include "ajreg.h"
++#include <string.h>
+
+
+
+--- EMBOSS-6.6.0/ajax/core/ajseqtype.c
++++ EMBOSS-6.6.0/ajax/core/ajseqtype.c
+@@ -32,7 +32,7 @@
+ #include "ajfeat.h"
+ #include "ajfile.h"
+ #include "ajreg.h"
+-
++#include <string.h>
+
+
+
+--- EMBOSS-6.6.0/nucleus/embindex.c
++++ EMBOSS-6.6.0/nucleus/embindex.c
+@@ -35,6 +35,7 @@
+ #include "ajnam.h"
+
+ #include <errno.h>
++#include <string.h>
+
+ #define BTENTRYFILE ".ent"
+ #define KWLIMIT 12
+--- EMBOSS-6.6.0/nucleus/embword.c
++++ EMBOSS-6.6.0/nucleus/embword.c
+@@ -36,7 +36,7 @@
+ #include "ajutil.h"
+
+ #include <math.h>
+-
++#include <string.h>
+
+
+
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-1 b/sci-biology/emboss/files/emboss-README.Gentoo-1
new file mode 100644
index 000000000000..81e71988ae80
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-1
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+ # cd /usr/share/EMBOSS/data
+ # ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+ # cd /usr/share/EMBOSS/data
+ # ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2
new file mode 100644
index 000000000000..72fa3662c9a8
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-2
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+ # cd EPREFIX/usr/share/EMBOSS/data
+ # ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+ # cd EPREFIX/usr/share/EMBOSS/data
+ # ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
new file mode 100644
index 000000000000..3af936dc1564
--- /dev/null
+++ b/sci-biology/emboss/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ EMBOSS is "The European Molecular Biology Open Software Suite".
+ EMBOSS is a free Open Source software analysis package specially
+ developed for the needs of the molecular biology (e.g. EMBnet) user
+ community. The software automatically copes with data in a variety
+ of formats and even allows transparent retrieval of sequence data
+ from the web. Also, as extensive libraries are provided with the
+ package, it is a platform to allow other scientists to develop and
+ release software in true open source spirit. EMBOSS also integrates
+ a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend
+ towards commercial software packages.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
new file mode 100644
index 000000000000..015da1fb031b
--- /dev/null
+++ b/sci-biology/eugene/Manifest
@@ -0,0 +1 @@
+DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4
diff --git a/sci-biology/eugene/eugene-4.1.ebuild b/sci-biology/eugene/eugene-4.1.ebuild
new file mode 100644
index 000000000000..088ecc7a1a8b
--- /dev/null
+++ b/sci-biology/eugene/eugene-4.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
+SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1157/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+DEPEND="
+ media-libs/gd[png]
+ media-libs/libpng:0=
+ "
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+src_prepare() {
+ # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
+ epatch \
+ "${FILESDIR}"/${PN}-3.6-overflow.patch \
+ "${FILESDIR}"/${PN}-3.6-plugins.patch \
+ "${FILESDIR}"/${P}-format-security.patch
+ sed \
+ -e '/SUBDIRS/ s/doc//' \
+ -e '/INSTALL.*doc/ s/\(.*\)//' \
+ -i Makefile.am || die
+ eautoreconf
+}
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
new file mode 100644
index 000000000000..7222530ad771
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-overflow.patch
@@ -0,0 +1,13 @@
+http://bugs.gentoo.org/show_bug.cgi?id=336607
+
+--- eugene-3.6/src/Sensor.cc
++++ eugene-3.6/src/Sensor.cc
+@@ -224,7 +224,7 @@
+ //--------------------------
+ void Signals :: PrintS ()
+ {
+- char t[7];
++ char t[10];
+ char s = '+';
+
+ switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
new file mode 100644
index 000000000000..1e910a13d5b1
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch
@@ -0,0 +1,43 @@
+http://bugs.gentoo.org/show_bug.cgi?id=297536
+
+--- eugene-3.6/src/Makefile.am
++++ eugene-3.6/src/Makefile.am
+@@ -20,7 +20,7 @@
+
+ SUBDIRS = Parametrization GDIF . SensorPlugins
+
+-AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
++AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
+ AM_CFLAGS =
+
+ bin_PROGRAMS = eugene
+--- eugene-3.6/src/MSensor.cc
++++ eugene-3.6/src/MSensor.cc
+@@ -97,7 +97,7 @@
+ std::string use_name;
+
+ if (!IsInitialized) {
+- PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
++ PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
+
+ // On rcupre les couples nom de sensor/priorit du .par
+ PAR.ResetIter();
+--- eugene-3.6/Makefile.am
++++ eugene-3.6/Makefile.am
+@@ -125,7 +125,7 @@
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
+- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
+@@ -144,6 +144,6 @@
+ $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
+ $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
+ $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
+- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins
++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins
+ $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
+ $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
new file mode 100644
index 000000000000..e6e4a6cc8bd7
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch
@@ -0,0 +1,16 @@
+ src/Hits.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Hits.cc b/src/Hits.cc
+index edfe178..b228be6 100755
+--- a/src/Hits.cc
++++ b/src/Hits.cc
+@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
+ while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
+ &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
+ {
+- if (HSP) fprintf(stderr,HSP);
++ if (HSP) fprintf(stderr, "%s", HSP);
+ if (phase < 0 && deb > fin)
+ {
+ int tmp = deb;
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/eugene/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
new file mode 100644
index 000000000000..3619350ee4d0
--- /dev/null
+++ b/sci-biology/exonerate/Manifest
@@ -0,0 +1 @@
+DIST exonerate-2.2.0.tar.gz 509870 SHA256 0ea2720b1388fa329f889522f43029b416ae311f57b229129a65e779616fe5ff SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c WHIRLPOOL dd7ba7a94b93f41d5ddbc66cc14740973dde20e875f37814229614c85312dcc1de031faab5153bc28be3284144d0f8451bd5e5115f8d9e312e4f88d771ce620c
diff --git a/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild
new file mode 100644
index 000000000000..966f7c2f8e01
--- /dev/null
+++ b/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils toolchain-funcs
+
+DESCRIPTION="Generic tool for pairwise sequence comparison"
+HOMEPAGE="http://www.ebi.ac.uk/~guy/exonerate/"
+SRC_URI="http://www.ebi.ac.uk/~guy/exonerate/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos"
+IUSE="utils test threads"
+
+REQUIRED_USE="test? ( utils )"
+
+DEPEND="dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
+
+src_prepare() {
+ tc-export CC
+ sed \
+ -e 's: -O3 -finline-functions::g' \
+ -i configure.in || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable utils utilities)
+ $(use_enable threads pthreads)
+ --enable-largefile
+ --enable-glib2
+ )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+ doman doc/man/man1/*.1
+}
diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
new file mode 100644
index 000000000000..3268055cd544
--- /dev/null
+++ b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
@@ -0,0 +1,15 @@
+Fix build with --as-needed
+
+https://bugs.gentoo.org/268094
+
+--- configure.in
++++ configure.in
+@@ -289,7 +289,7 @@
+ if test "$enable_pthreads" = yes; then
+ echo "Using PTHREADS"
+ CFLAGS="$CFLAGS -DUSE_PTHREADS"
+- LDFLAGS="$LDFLAGS -lpthread"
++ LIBS="$LIBS -lpthread"
+ elif test "$enable_pthreads" = no; then
+ echo "Not using pthreads"
+ else
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
new file mode 100644
index 000000000000..711d805d77e7
--- /dev/null
+++ b/sci-biology/exonerate/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>je_fro@gentoo.org</email>
+ <name>Jeff Gardner</name>
+ </maintainer>
+ <longdescription lang="en">
+ exonerate is a generic tool for pairwise sequence comparison
+ </longdescription>
+ <use>
+ <flag name="utils">Install all utilities</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest
new file mode 100644
index 000000000000..6edb1d9f6603
--- /dev/null
+++ b/sci-biology/express/Manifest
@@ -0,0 +1,2 @@
+DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403 WHIRLPOOL 290772dceca2465f922f5d5fe548dc8fd460422589697173c58f98dc3afa2e91175fe1fa52e5f29458ea6af74c8da609776fa583bf5efcb2d5771c4c9ad51cde
+DIST express-1.5.1-src.tgz 931166 SHA256 0c5840a42da830fd8701dda8eef13f4792248bab4e56d665a0e2ca075aff2c0f SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee WHIRLPOOL 2c75385b2a2ec8f7b77df760344affc108e827eb9f59014f08af0cee0ca8806beeba101d13ed8b43883a25fc9486bd405f402339f0e4e394d3895694c75a4e2a
diff --git a/sci-biology/express/express-0.9.5-r1.ebuild b/sci-biology/express/express-0.9.5-r1.ebuild
new file mode 100644
index 000000000000..608ade0766ea
--- /dev/null
+++ b/sci-biology/express/express-0.9.5-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Streaming RNA-Seq Analysis"
+HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
+SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ >=dev-libs/boost-1.52.0:=
+ sys-libs/zlib
+ sci-biology/bamtools"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-src"
+
+CMAKE_USE_DIR="${S}/src"
+
+src_prepare() {
+ sed \
+ -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \
+ -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \
+ -e '1 a find_package(ZLIB)' \
+ -e '/add_executable/ a include_directories("/usr/include/bamtools")' \
+ -i src/CMakeLists.txt || die
+
+ cmake-utils_src_prepare
+}
diff --git a/sci-biology/express/express-0.9.5.ebuild b/sci-biology/express/express-0.9.5.ebuild
new file mode 100644
index 000000000000..a4fcff4be4f5
--- /dev/null
+++ b/sci-biology/express/express-0.9.5.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit cmake-utils
+
+DESCRIPTION="Streaming RNA-Seq Analysis"
+HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
+SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ dev-libs/boost
+ sys-libs/zlib
+ sci-biology/bamtools"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-src"
+
+CMAKE_USE_DIR="${S}/src"
+
+src_prepare() {
+ sed \
+ -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \
+ -e '1 a find_package(Boost 1.46 COMPONENTS filesystem program_options thread)' \
+ -e '1 a find_package(ZLIB)' \
+ -e '/add_executable/ a include_directories("/usr/include/bamtools")' \
+ -i src/CMakeLists.txt || die
+}
diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
new file mode 100644
index 000000000000..231b1f878ba3
--- /dev/null
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Streaming RNA-Seq Analysis"
+HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
+SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ >=dev-libs/boost-1.52.0:=
+ dev-libs/protobuf
+ dev-util/google-perftools
+ sys-libs/zlib
+ sci-biology/bamtools"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-src"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-buildsystem.patch
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools"
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch
new file mode 100644
index 000000000000..fca5feadd111
--- /dev/null
+++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch
@@ -0,0 +1,55 @@
+ CMakeLists.txt | 8 +++-----
+ src/CMakeLists.txt | 4 ++--
+ 2 files changed, 5 insertions(+), 7 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c768e28..65d5633 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
+ set(${PROJECT_NAME}_VERSION_MINOR 5)
+ set(${PROJECT_NAME}_VERSION_PATCH 1)
+
+-set(CMAKE_CXX_FLAGS "-Wall")
+-
+ set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
+ set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}")
+ set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}")
+
+ set(CMAKE_BUILD_TYPE Release)
+-set(Boost_USE_STATIC_LIBS ON)
++set(Boost_USE_STATIC_LIBS OFF)
+
+ find_package(Boost 1.39
+ COMPONENTS
+@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
+
+ find_package(Protobuf)
+ if (PROTOBUF_FOUND)
+- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include")
++ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE})
+ set(PROTO_INT 1)
+ else (PROTOBUF_FOUND)
+- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include")
++ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE})
+ set(PROTO_INT 0)
+ endif(PROTOBUF_FOUND)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 1cc0c01..8929d1f 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC)
+ if(WIN32)
+ set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
+ else(WIN32)
+- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread")
++ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread")
+ endif(WIN32)
+
+ if (PROTOBUF_FOUND)
+- set(LIBRARIES ${LIBRARIES} "libprotobuf.a")
++ set(LIBRARIES ${LIBRARIES} "protobuf")
+ endif(PROTOBUF_FOUND)
+
+ target_link_libraries(express ${LIBRARIES})
diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/express/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
new file mode 100644
index 000000000000..734131ee7f78
--- /dev/null
+++ b/sci-biology/fasta/Manifest
@@ -0,0 +1,2 @@
+DIST fasta-35.4.10.tar.gz 618971 SHA256 60616963093784d2e41ff9c125d68d7a43bbe411cdef8dc37ce922b4c3aec758 SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47 WHIRLPOOL 87eb008bc507923ceaebe93c5eb2ab367ca184c0fa2304491ba8edf09e5f6eabe16a8823a1b6a11d5157355406157d1c97da9bd1e194dc26709188b995a386ce
+DIST fasta-36.3.5e.tar.gz 943763 SHA256 92f44a0e0e13bcd6782489f2db42044d7109a9071d775fb0435df24288be90c2 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 WHIRLPOOL 803cee2c7da8487811b6aa9776bfa737ab35c4de2f76887915ab285802a738cb073059f4122379512195bd54ad63db42c61059587b6a2aa34550774e57f9f5fa
diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild
new file mode 100644
index 000000000000..3fb4fb923a98
--- /dev/null
+++ b/sci-biology/fasta/fasta-35.4.10.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+ CC_ALT=
+ CFLAGS_ALT=
+ ALT=
+
+ use debug && append-flags -DDEBUG
+
+ if [[ $(tc-getCC) == *icc* ]]; then
+ CC_ALT=icc
+ ALT="${ALT}_icc"
+ else
+ CC_ALT=$(tc-getCC)
+ use x86 && ALT="32"
+ use amd64 && ALT="64"
+ fi
+
+ if use cpu_flags_x86_sse2 ; then
+ ALT="${ALT}_sse2"
+ append-flags -msse2
+ [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+ fi
+
+ export CC_ALT="${CC_ALT}"
+ export ALT="${ALT}"
+
+ epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+ cd src
+ emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die
+}
+
+src_install() {
+ dobin bin/* || die
+ doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
+ dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
+}
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
new file mode 100644
index 000000000000..a9466820c4e8
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+ CC_ALT=
+ CFLAGS_ALT=
+ ALT=
+
+ use debug && append-flags -DDEBUG
+
+ if [[ $(tc-getCC) == *icc* ]]; then
+ CC_ALT=icc
+ ALT="${ALT}_icc"
+ else
+ CC_ALT=$(tc-getCC)
+ use x86 && ALT="32"
+ use amd64 && ALT="64"
+ fi
+
+ if use cpu_flags_x86_sse2 ; then
+ ALT="${ALT}_sse2"
+ append-flags -msse2
+ [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+ fi
+
+ export CC_ALT="${CC_ALT}"
+ export ALT="${ALT}"
+
+ epatch "${FILESDIR}"/${P}-ldflags.patch
+
+ sed \
+ -e 's:-ffast-math::g' \
+ -i make/Makefile* || die
+
+}
+
+src_compile() {
+ cd src || die
+ emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+}
+
+src_test() {
+ cd test || die
+ FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+ local bin
+ dobin bin/*
+
+ pushd bin > /dev/null || die
+ for bin in *36; do
+ dosym ${bin} /usr/bin/${bin%36} || die
+ done
+ popd
+
+ insinto /usr/share/${PN}
+ doins -r conf/* data seq
+
+ doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+ dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+}
diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch
new file mode 100644
index 000000000000..c3b7a9b56904
--- /dev/null
+++ b/sci-biology/fasta/files/35.4.10-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index a808667..405be95 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+
+ map_db : map_db.c uascii.h ncbl2_head.h
+- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+
+ list_db : list_db.c
+- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+
+ lav2ps : lav2plt.o lavplt_ps.o
+- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+
+ lav2svg : lav2plt.o lavplt_svg.o
+- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
+
+ res_stats : res_stats.o scale_se.o
+- $(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
new file mode 100644
index 000000000000..a6eeabfdf46c
--- /dev/null
+++ b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
@@ -0,0 +1,74 @@
+ make/Makefile.pcom | 8 ++++----
+ make/Makefile.pcom_s | 8 ++++----
+ make/Makefile.pcom_t | 8 ++++----
+ 3 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index 9c5f801..33fc001 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+
+ map_db : map_db.c uascii.h ncbl2_head.h
+- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+
+ list_db : list_db.c
+- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+
+
+ lav2ps : lav2plt.o lavplt_ps.o
+- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+
+ lav2svg : lav2plt.o lavplt_svg.o
+- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s
+index dc53001..8a45044 100644
+--- a/make/Makefile.pcom_s
++++ b/make/Makefile.pcom_s
+@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+
+ map_db : map_db.c uascii.h ncbl2_head.h
+- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+
+ list_db : list_db.c
+- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+
+
+ lav2ps : lav2plt.o lavplt_ps.o
+- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+
+ lav2svg : lav2plt.o lavplt_svg.o
+- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t
+index 8a71438..5b08a50 100644
+--- a/make/Makefile.pcom_t
++++ b/make/Makefile.pcom_t
+@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+
+ map_db : map_db.c uascii.h ncbl2_head.h
+- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+
+ list_db : list_db.c
+- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+
+
+ lav2ps : lav2plt.o lavplt_ps.o
+- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+
+ lav2svg : lav2plt.o lavplt_svg.o
+- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
new file mode 100644
index 000000000000..b98c9919d241
--- /dev/null
+++ b/sci-biology/fasta/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>je_fro@gentoo.org</email>
+ <name>Jeff Gardner</name>
+ </maintainer>
+ <longdescription lang="en">
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
new file mode 100644
index 000000000000..da5370b6e7de
--- /dev/null
+++ b/sci-biology/fasttree/Manifest
@@ -0,0 +1,6 @@
+DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775
+DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 WHIRLPOOL 31331c85584c2030f56955e79250c6d6c06147007c6dd10f324c207fdebd4a1b89c87dcce52e5bab6e8d89cc69656d95a51bd808f52b8d61f6d29af40a5d4976
+DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
+DIST FastTreeUPGMA-2.1.8.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
+DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
+DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild
new file mode 100644
index 000000000000..522d09f60400
--- /dev/null
+++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
+HOMEPAGE="http://www.microbesonline.org/fasttree/"
+SRC_URI="
+ http://www.microbesonline.org/fasttree/FastTree-${PV}.c
+ http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
+ http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="double-precision openmp cpu_flags_x86_sse3"
+
+REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
+
+DOCS=( README )
+
+PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
+
+src_unpack() {
+ mkdir "${S}" || die
+ cd "${S}" || die
+ unpack ${A}
+ cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
+}
+
+src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt . || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DVERSION="${PV}"
+ $(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
+ $(cmake-utils_use_use openmp)
+ $(cmake-utils_use_use double-precision double)
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild
new file mode 100644
index 000000000000..fea83a4d7696
--- /dev/null
+++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
+HOMEPAGE="http://www.microbesonline.org/fasttree/"
+SRC_URI="
+ http://www.microbesonline.org/fasttree/FastTree-${PV}.c
+ http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
+ http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="double-precision openmp cpu_flags_x86_sse3"
+
+REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
+
+DOCS=( README )
+
+PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
+
+src_unpack() {
+ mkdir "${S}" || die
+ cd "${S}" || die
+ unpack ${A}
+ cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
+}
+
+src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt . || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DVERSION="${PV}"
+ $(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
+ $(cmake-utils_use_use openmp)
+ $(cmake-utils_use_use double-precision double)
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt
new file mode 100644
index 000000000000..e7c53afdaf36
--- /dev/null
+++ b/sci-biology/fasttree/files/CMakeLists.txt
@@ -0,0 +1,30 @@
+cmake_minimum_required (VERSION 2.6)
+project(fasttree C)
+
+option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON)
+option(USE_DOUBLE "Use double precission" OFF)
+option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON)
+
+if(USE_OPENMP)
+ SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" )
+ SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" )
+endif(USE_OPENMP)
+
+if(USE_DOUBLE)
+ SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" )
+endif(USE_DOUBLE)
+
+if(NOT HAS_SSE3)
+ SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" )
+endif(NOT HAS_SSE3)
+
+
+add_executable(FastTree FastTree-${VERSION}.c)
+add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c)
+
+target_link_libraries(FastTree m)
+target_link_libraries(FastTreeUPGMA m)
+
+install (TARGETS FastTree FastTreeUPGMA DESTINATION bin)
+
+install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree)
diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
new file mode 100644
index 000000000000..31dafdad46de
--- /dev/null
+++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
@@ -0,0 +1,25 @@
+ FastTreeUPGMA-2.1.7.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c
+index af76cb1..4065f42 100644
+--- a/FastTreeUPGMA-2.1.7.c
++++ b/FastTreeUPGMA-2.1.7.c
+@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
+ break;
+ }
+ if(iArg < argc-1) {
+- fprintf(stderr, usage);
++ fprintf(stderr, "%s", usage);
+ exit(1);
+ }
+
+@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
+ assert(first >= 0);
+ /* Print the name, or the subtree of duplicate names */
+ if (nameNext[first] == -1) {
+- fprintf(fp, names[uniqueFirst[node]]);
++ fprintf(fp, "%s", names[uniqueFirst[node]]);
+ } else {
+ fprintf(fp,"(%s:0.0",names[first]);
+ int iName = nameNext[first];
diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
new file mode 100644
index 000000000000..15f5c174ec40
--- /dev/null
+++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
@@ -0,0 +1,25 @@
+ FastTreeUPGMA-2.1.8.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
+index af76cb1..4065f42 100644
+--- a/FastTreeUPGMA-2.1.8.c
++++ b/FastTreeUPGMA-2.1.8.c
+@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
+ break;
+ }
+ if(iArg < argc-1) {
+- fprintf(stderr, usage);
++ fprintf(stderr, "%s", usage);
+ exit(1);
+ }
+
+@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
+ assert(first >= 0);
+ /* Print the name, or the subtree of duplicate names */
+ if (nameNext[first] == -1) {
+- fprintf(fp, names[uniqueFirst[node]]);
++ fprintf(fp, "%s", names[uniqueFirst[node]]);
+ } else {
+ fprintf(fp,"(%s:0.0",names[first]);
+ int iName = nameNext[first];
diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml
new file mode 100644
index 000000000000..5ee1f51e55df
--- /dev/null
+++ b/sci-biology/fasttree/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="double-precision">
+ use double precision instead of single-precision floating point
+ (2x memroy required)
+ </flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest
new file mode 100644
index 000000000000..618173a8779c
--- /dev/null
+++ b/sci-biology/finchtv/Manifest
@@ -0,0 +1 @@
+DIST finchtv_1_3_1.tar.gz 6706911 SHA256 03fccbf1ab09b571bbf55d0b71dd86975513b7a6c8d54795055a184b4eda8858 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8 WHIRLPOOL 3b6de1673b69bfb41f1416e7758ccafcf97f10bd4f348a88e8498d04c408caf2ac316d8e1a20bf1abe2d6487f38c3b9875af54ecb1d2b1a2ff813b436de90988
diff --git a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild
new file mode 100644
index 000000000000..8f89b5cbc873
--- /dev/null
+++ b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PV="${PV//./_}"
+MY_P=${PN}_${MY_PV}
+
+DESCRIPTION="Graphical viewer for chromatogram files"
+HOMEPAGE="http://www.geospiza.com/finchtv/"
+SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz"
+
+LICENSE="finchtv"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}/${MY_P}"
+
+QA_PREBUILT="opt/bin/*"
+
+src_install() {
+ exeinto /opt/bin
+ doexe finchtv
+ dodoc ReleaseNotes.txt
+ dohtml -r Help/*
+ insinto /usr/share/doc/${PN}
+ doins -r SampleData
+}
diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml
new file mode 100644
index 000000000000..e487463fc00b
--- /dev/null
+++ b/sci-biology/finchtv/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>je_fro@gentoo.org</email>
+ <name>Jeff Gardner</name>
+ </maintainer>
+ <longdescription lang="en">
+A cross-platform graphical viewer for chromatogram files.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/flower/Manifest b/sci-biology/flower/Manifest
new file mode 100644
index 000000000000..727ec9661be4
--- /dev/null
+++ b/sci-biology/flower/Manifest
@@ -0,0 +1 @@
+DIST flower-0.7.2.tar.gz 10455 SHA256 0b8d60e8af5114e496e401af344c3f7338ecb42c1b8b8a96220efa19d21a3465 SHA512 1c96173b8e3a881b2c65f3dcabd27e71a9341a73e56c056534e7d8eb53bc3222d8d32c6397a3a80413ee361bce42a40f20d7280d5e9748a1c1b828d42fefba74 WHIRLPOOL 8fec1ce45acb41e3da63eee27911fa7a738c7b9e259cecdc01df1f1c06974099b50505a0e51c041e8ae96f60cff9a283aa2b887d12cf7a800b1a129d2cc0ad0c
diff --git a/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch
new file mode 100644
index 000000000000..90dfb2326918
--- /dev/null
+++ b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch
@@ -0,0 +1,27 @@
+diff --git a/src/Flower.hs b/src/Flower.hs
+index fca5814..9424222 100644
+--- a/src/Flower.hs
++++ b/src/Flower.hs
+@@ -25,6 +25,7 @@ import qualified Data.ByteString.Lazy as L1
+
+ import Data.Array.Unboxed
+ import Data.Array.ST
++import qualified Data.Array.Unsafe as U
+ import Control.Monad.ST
+ import Control.Monad.State
+
+@@ -238,10 +239,10 @@ histogram fl scores = runST $ do
+ ins1 (x,_) = error ("Illegal character "++show x++" in flow!")
+ bump ar i = readArray ar i >>= \x -> writeArray ar i (x+1)
+ mapM_ ins1 (zip (cycle fl) (map (\x->if x>9999 || x<0 then 9999 else x) $ concat scores))
+- a' <- unsafeFreeze a
+- c' <- unsafeFreeze c
+- g' <- unsafeFreeze g
+- t' <- unsafeFreeze t
++ a' <- U.unsafeFreeze a
++ c' <- U.unsafeFreeze c
++ g' <- U.unsafeFreeze g
++ t' <- U.unsafeFreeze t
+ return (a',c',g',t')
+
+ showHist :: (Hist,Hist,Hist,Hist) -> String
diff --git a/sci-biology/flower/flower-0.7.2.ebuild b/sci-biology/flower/flower-0.7.2.ebuild
new file mode 100644
index 000000000000..25e24c3aa26f
--- /dev/null
+++ b/sci-biology/flower/flower-0.7.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+# ebuild generated by hackport 0.2.17.9999
+
+EAPI=5
+
+CABAL_FEATURES="bin"
+inherit eutils haskell-cabal
+
+DESCRIPTION="Analyze 454 flowgrams (.SFF files)"
+HOMEPAGE="http://biohaskell.org/Applications/Flower"
+SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ >=dev-haskell/binary-0.4 <dev-haskell/binary-0.8
+ >=dev-haskell/bio-0.4.9
+ >=dev-haskell/cabal-1.6
+ >=dev-haskell/cmdargs-0.5
+ dev-haskell/mtl
+ dev-haskell/random
+ >=dev-lang/ghc-6.10.1"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-ghc-7.8.patch
+ cabal_chdeps \
+ 'binary == 0.4.*' 'binary >= 0.4 && <0.8'
+}
diff --git a/sci-biology/flower/metadata.xml b/sci-biology/flower/metadata.xml
new file mode 100644
index 000000000000..dcaae2095b0e
--- /dev/null
+++ b/sci-biology/flower/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>haskell</herd>
+ <maintainer>
+ <email>haskell@gentoo.org</email>
+ </maintainer>
+ <longdescription>
+ flower - FLOWgram ExtractoR tools
+
+ The flower executable reads files in SFF-format and produces various output,
+ including sequences with quality, or flowgram data in tabular format. By default,
+ it outputs a textual representation of the data in the SFF-file, much like
+ &#39;sffinfo&#39; from Roche does.
+
+ The fselect executable extracts reads from SFF-files, generating a new
+ SFF-file with a subset of the reads based on various criteria.
+
+ Sometimes SFF files will appear to be corrupted, with all-zero blocks in the
+ file. The frecover program ignores these and tries to resync with the file after an
+ invalid region. This was likely a one-time bug in the 454 software, so this program
+ is probably not so useful any more.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
new file mode 100644
index 000000000000..46799da48482
--- /dev/null
+++ b/sci-biology/foldingathome/Manifest
@@ -0,0 +1,4 @@
+DIST fahclient_7.3.6-32bit-release.tar.bz2 4014455 SHA256 c8415aa5a64d6b26e7684327d51f9133d524777d4123ea47138ba86595c37f12 SHA512 0a49e9cb26659357b4855f5aaf7ef5c078f172af16777d74fb566e7faa61ac0e41185dcd6f06841bf4efe047017e8dc783eae7682a40b921acb436e4d81e6639 WHIRLPOOL 0cd8f0b6dcfce297cb70b307887f1d44278c07435f5a067d9f1e83399b3913710d481982033023faf1b9056b63f14eca3b53babe698633de24544c6cdbce5f82
+DIST fahclient_7.3.6-64bit-release.tar.bz2 4349503 SHA256 e3d48b0d1b64da96601f741e0b9164ea633f1be3fe4407086679bc7c72742079 SHA512 9995a72549e38724830c403eef188786b137c8669b6121c0ec6c3d29539db9b0f67876adf5c3af64c818ada05f57a0f2ea88a58b73bdfd852c1ed8f09a327583 WHIRLPOOL 4e5bccb175dc042a1380c06b96a5d803f36ede50e429d3b1f13b33c872f753bda5acd7f5a3d60a522cb82c7da47313ef95e0c55778cbe94d579a9ecaa22c49cc
+DIST fahclient_7.4.4-32bit-release.tar.bz2 4313096 SHA256 81f1a1d161d1302a08638f23ebcfd7a163046a5427c49c70651fc8e2f6d8d60e SHA512 6a660b99c97c83518863ef671ae760b15e3ca33cacfde6485c11b29e98fab15a9d27833ba307c95b39e6ffb7f271cd0c7a47060ec5b8614961e9a5ee46494b3f WHIRLPOOL 6c6c25446e8e118b7931c58643827739691bcb9f1ae67461e6dd72cfc8556f86d49c533669897f6711537ce920680c23d0d496ba75a21047a88708cc93fec314
+DIST fahclient_7.4.4-64bit-release.tar.bz2 4451080 SHA256 4642ed9b5a06c8ab63106293f6a5ce547f6a96efe85fcd3b8c19d9065ab582df SHA512 40fc93c4ec682342040a4c7a9fd92dc9d1727ef60af6d3fa3191575719c7e595868f289727561f6902f8374061f7b51dfcf565ac047706336ef4ae9a589ff9a8 WHIRLPOOL 4feea83f1e826430943dec0495ce7658408cdaa4671bf1e4d1ec338991dbeb1599f25a4835f3960bea135fe4af7c4e415be6767ea5a0a13f63201c64e6ce6f6e
diff --git a/sci-biology/foldingathome/files/7.3/fah-init b/sci-biology/foldingathome/files/7.3/fah-init
new file mode 100644
index 000000000000..1c1a232fb697
--- /dev/null
+++ b/sci-biology/foldingathome/files/7.3/fah-init
@@ -0,0 +1,30 @@
+#!/sbin/runscript
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $
+
+extra_commands="unitinfo"
+
+unitinfo() {
+ einfo "$(head -n1 /opt/foldingathome/unitinfo.txt):"
+ sed -e '1,2d' /opt/foldingathome/unitinfo.txt
+}
+
+start() {
+ ebegin "Starting Folding@Home"
+ cd /opt/foldingathome
+ start-stop-daemon --chdir ${PWD} --user foldingathome --nicelevel 19 \
+ --make-pidfile --pidfile "${PIDFILE}" \
+ --start --background --exec ./FAHClient -- ${FOLD_OPTS}
+ eend $?
+}
+
+stop() {
+ ebegin "Stopping Folding@Home"
+ start-stop-daemon --stop --user foldingathome --pidfile "${PIDFILE}"
+ if [ $? -ne 0 ]; then
+ killall --user foldingathome --signal SIGKILL
+ ewarn "killing all processes running as user 'foldingathome' ..."
+ fi
+ eend $?
+}
diff --git a/sci-biology/foldingathome/files/7.3/folding-conf.d b/sci-biology/foldingathome/files/7.3/folding-conf.d
new file mode 100644
index 000000000000..b4e0448226a6
--- /dev/null
+++ b/sci-biology/foldingathome/files/7.3/folding-conf.d
@@ -0,0 +1,10 @@
+# Config file for /etc/init.d/foldingathome
+#
+# The f@h client configuration can be found in /opt/foldingathome/config.xml
+# Run /opt/foldingathome/initfolding to reconfigure that.
+#
+# The options that may be passed to the Folding client can be obtained
+# by running /opt/foldingathome/FAHClient --help
+#
+FOLD_OPTS=""
+PIDFILE=/run/folding
diff --git a/sci-biology/foldingathome/files/7.3/initfolding b/sci-biology/foldingathome/files/7.3/initfolding
new file mode 100644
index 000000000000..240b7fa2f17b
--- /dev/null
+++ b/sci-biology/foldingathome/files/7.3/initfolding
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+cd /opt/foldingathome
+/opt/foldingathome/FAHClient --configure
+/bin/chown -R foldingathome:nogroup /opt/foldingathome
diff --git a/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild b/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild
new file mode 100644
index 000000000000..d55a4d1c9140
--- /dev/null
+++ b/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit versionator user
+
+MY_BASEURI="https://fah.stanford.edu/file-releases/public/release/fahclient"
+MY_64B_URI="${MY_BASEURI}/centos-5.3-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2"
+MY_32B_URI="${MY_BASEURI}/centos-5.5-32bit/v$(get_version_component_range 1-2)/fahclient_${PV}-32bit-release.tar.bz2"
+
+DESCRIPTION="Folding@Home is a distributed computing project for protein folding"
+HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html"
+SRC_URI="x86? ( ${MY_32B_URI} )
+ amd64? ( ${MY_64B_URI} )"
+
+RESTRICT="mirror bindist strip"
+
+LICENSE="FAH-EULA-2009 FAH-special-permission"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Expressly listing all deps, as this is a binpkg and it is doubtful whether
+# i.e. uclibc or clang can provide what is necessary at runtime
+RDEPEND="app-arch/bzip2
+ sys-devel/gcc
+ sys-libs/glibc
+ sys-libs/zlib"
+
+S="${WORKDIR}"
+
+I="opt/foldingathome"
+
+QA_PREBUILT="${I}/*"
+
+pkg_setup() {
+ I="${EROOT}/${I}"
+ einfo ""
+ cat "${PORTDIR}"/licenses/FAH-special-permission
+ einfo ""
+}
+
+src_install() {
+ local myS="fahclient_${PV}-64bit-release"
+ use x86 && myS="${myS//64bit/32bit}"
+ exeinto "${I}"
+ doexe "${FILESDIR}"/$(get_version_component_range 1-2)/initfolding
+ doexe "${myS}"/{FAHClient,FAHCoreWrapper}
+ newconfd "${FILESDIR}"/$(get_version_component_range 1-2)/folding-conf.d foldingathome
+ newinitd "${FILESDIR}"/$(get_version_component_range 1-2)/fah-init foldingathome
+}
+
+pkg_preinst() {
+ # the bash shell is important for "su -c" in init script
+ enewuser foldingathome -1 /bin/bash /opt/foldingathome
+}
+
+pkg_postinst() {
+ chown -R foldingathome:nogroup "${I}"
+ einfo "To run Folding@home in the background at boot:"
+ einfo "\trc-update add foldingathome default"
+ einfo ""
+ if [ ! -e "${I}"/config.xml ]; then
+ elog "No configuration found -- please run ${I}/initfolding or"
+ elog "emerge --config ${P} to configure your client and edit"
+ elog "${EROOT}/etc/conf.d/foldingathome for options"
+ fi
+ einfo ""
+ einfo "The original author encourages you to acquire a username and join team 36480."
+ einfo "http://folding.stanford.edu/English/Download#ntoc2"
+ einfo ""
+}
+
+pkg_postrm() {
+ elog "Folding@home data files were not removed."
+ elog "Remove them manually from ${I}"
+}
+
+pkg_config() {
+ "${I}"/initfolding
+}
diff --git a/sci-biology/foldingathome/foldingathome-7.4.4.ebuild b/sci-biology/foldingathome/foldingathome-7.4.4.ebuild
new file mode 100644
index 000000000000..2a48c1b03554
--- /dev/null
+++ b/sci-biology/foldingathome/foldingathome-7.4.4.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit versionator user
+
+MY_BASEURI="https://fah.stanford.edu/file-releases/public/release/fahclient"
+MY_64B_URI="${MY_BASEURI}/centos-5.3-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2"
+MY_32B_URI="${MY_BASEURI}/centos-5.5-32bit/v$(get_version_component_range 1-2)/fahclient_${PV}-32bit-release.tar.bz2"
+
+DESCRIPTION="Folding@Home is a distributed computing project for protein folding"
+HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html"
+SRC_URI="x86? ( ${MY_32B_URI} )
+ amd64? ( ${MY_64B_URI} )"
+
+RESTRICT="mirror bindist strip"
+
+LICENSE="FAH-EULA-2014 FAH-special-permission"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Expressly listing all deps, as this is a binpkg and it is doubtful whether
+# i.e. uclibc or clang can provide what is necessary at runtime
+RDEPEND="app-arch/bzip2
+ sys-devel/gcc
+ sys-libs/glibc
+ sys-libs/zlib"
+
+S="${WORKDIR}"
+
+I="opt/foldingathome"
+
+QA_PREBUILT="${I}/*"
+
+pkg_setup() {
+ I="${EROOT}/${I}"
+ einfo ""
+ cat "${PORTDIR}"/licenses/FAH-special-permission
+ einfo ""
+}
+
+src_install() {
+ local myS="fahclient_${PV}-64bit-release"
+ use x86 && myS="${myS//64bit/32bit}"
+ exeinto "${I}"
+ doexe "${FILESDIR}"/7.3/initfolding
+ doexe "${myS}"/{FAHClient,FAHCoreWrapper}
+ newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome
+ newinitd "${FILESDIR}"/7.3/fah-init foldingathome
+}
+
+pkg_preinst() {
+ # the bash shell is important for "su -c" in init script
+ enewuser foldingathome -1 /bin/bash /opt/foldingathome
+}
+
+pkg_postinst() {
+ chown -R foldingathome:nogroup "${I}"
+ einfo "To run Folding@home in the background at boot (with openrc):"
+ einfo "\trc-update add foldingathome default"
+ einfo ""
+ if [ ! -e "${I}"/config.xml ]; then
+ elog "No configuration found -- please run ${I}/initfolding or"
+ elog "emerge --config ${P} to configure your client and edit"
+ elog "${EROOT}/etc/conf.d/foldingathome for options"
+ fi
+ einfo ""
+ einfo "The original author encourages you to acquire a username and join team 36480."
+ einfo "http://folding.stanford.edu/English/Download#ntoc2"
+ einfo ""
+}
+
+pkg_postrm() {
+ elog "Folding@home data files were not removed."
+ elog "Remove them manually from ${I}"
+}
+
+pkg_config() {
+ "${I}"/initfolding
+}
diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml
new file mode 100644
index 000000000000..63d767b84f60
--- /dev/null
+++ b/sci-biology/foldingathome/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+ <email>axs@gentoo.org</email>
+ <name>Ian Stakenvicius</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest
new file mode 100644
index 000000000000..6cd4e325d33f
--- /dev/null
+++ b/sci-biology/gatk/Manifest
@@ -0,0 +1 @@
+DIST gatk-2.4.tar.gz 9106774 SHA256 db0be90ef5182866a1f936742fba20b317ce582556e19acb69de2a8894f7383a SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace WHIRLPOOL 1fa7a73f317db82c313ea112ffaa6466c2b17384f1ad8d06c74a3f4764dfd822f036cc2dc99890c157fc2c32ce299a4a7d0c73cafc72dd7ad955d75053745b2c
diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild
new file mode 100644
index 000000000000..53bc0dc1b50b
--- /dev/null
+++ b/sci-biology/gatk/gatk-2.4.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit java-pkg-2 java-ant-2 vcs-snapshot
+
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
+SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND="
+ >=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND="
+ >=virtual/jre-1.6
+ ${COMMON_DEPS}"
+
+src_prepare() {
+ sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar dist/*.jar
+ java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
+ java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
+}
diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
new file mode 100644
index 000000000000..9a705487d658
--- /dev/null
+++ b/sci-biology/gatk/gatk-9999.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit git-2 java-pkg-2 java-ant-2
+
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+COMMON_DEPS=""
+DEPEND="
+ >=virtual/jdk-1.6
+ dev-vcs/git
+ ${COMMON_DEPS}"
+RDEPEND="
+ >=virtual/jre-1.6
+ ${COMMON_DEPS}"
+
+src_prepare() {
+ sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar dist/*.jar
+ java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
+ java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
+}
diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/gatk/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
new file mode 100644
index 000000000000..affcfb9f045f
--- /dev/null
+++ b/sci-biology/gibbs/Manifest
@@ -0,0 +1 @@
+DIST gibbs-3.1.tar.gz 563300 RMD160 063de85a7f1a62bcd63c0838db62cb344ff27abd SHA1 9e6fcddd6036ea0c19259820dcfffa9286cd4e1f SHA256 e8bd62b7d2580b00fc0cdf32ed75ac1ffac29747c75227269a75fd587ba77b69
diff --git a/sci-biology/gibbs/files/gibbs-demo b/sci-biology/gibbs/files/gibbs-demo
new file mode 100644
index 000000000000..c58ae3b88e04
--- /dev/null
+++ b/sci-biology/gibbs/files/gibbs-demo
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+gibbs /usr/share/gibbs/examples/porins.b185 11 100 -R2000 -s230
+gibbs /usr/share/gibbs/examples/iomps.b58 11 125 -s1
+gibbs /usr/share/gibbs/examples/Igfold.b60x 12,12,12 90,90,90 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 12 150 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 18,18,18 20,20,20 -s1
diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
new file mode 100644
index 000000000000..9ed11b435129
--- /dev/null
+++ b/sci-biology/gibbs/gibbs-3.1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils multilib
+
+DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
+HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
+SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="mpi"
+KEYWORDS="amd64 x86"
+
+DEPEND="
+ mpi? (
+ virtual/mpi
+ sys-cluster/mpe2 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ sed \
+ -e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \
+ -e 's/-Werror//' \
+ -i configure.in || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ if use mpi; then export CC=mpicc; fi
+ local myeconfargs=( $(use_enable mpi) )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+ exeinto /usr/$(get_libdir)/${PN}
+ doexe *.pl
+ dodoc README ChangeLog
+}
+
+pkg_postinst() {
+ einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}."
+ einfo "These scripts require installation of sci-biology/bioperl."
+}
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
new file mode 100644
index 000000000000..c31e2db70216
--- /dev/null
+++ b/sci-biology/gibbs/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ The Gibbs motif sampler stochastically examines candidate alignments
+ in an effort to find the best alignment as measured by the maximum
+ a posteriori (MAP) log-likelihood ratio.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
new file mode 100644
index 000000000000..7071ac856370
--- /dev/null
+++ b/sci-biology/glimmer/Manifest
@@ -0,0 +1,2 @@
+DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c WHIRLPOOL c3eedb4a3a65043a69d632360608f04382117b8f7f3718eae328a1aa14f9f5d6d9ae6f05e0a83a09af5eb9e6b0c7b0ae26cb820813341aa5d7fa3f6002938ce8
+DIST glimmer302b.tar.gz 5637975 SHA256 ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 WHIRLPOOL bbce6f57546e6cc77801ac7f5e783510feafc2e120a8727e848a95dd9e2d966538e56cb7be597c2a463d9b372c8586a389d639e1377708a27bd56f81b37fea1f
diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
new file mode 100644
index 000000000000..f6051ec82054
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
@@ -0,0 +1,24 @@
+diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
+--- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000
+@@ -443,7 +443,7 @@
+ // Return a subscript corresponding to character ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (CONVERSION_STRING, tolower (ch));
+ if (p == NULL)
+diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
+--- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000
+@@ -1981,7 +1981,7 @@
+ // model) for character ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+ if (p == NULL)
diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
new file mode 100644
index 000000000000..91498b116d12
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
@@ -0,0 +1,22 @@
+diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
+--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100
+@@ -2,12 +2,12 @@
+
+
+ all:
+- @ TGT=objs
+- @ $(dosubdirs)
+- @ TGT=libs
+- @ $(dosubdirs)
+- @ TGT=progs
+- @ $(dosubdirs)
++ @+ TGT=objs
++ @+ $(dosubdirs)
++ @+ TGT=libs
++ @+ $(dosubdirs)
++ @+ TGT=progs
++ @+ $(dosubdirs)
+
+
+ install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
new file mode 100644
index 000000000000..0a04fbef1dcc
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
@@ -0,0 +1,88 @@
+diff --git a/src/c_make.gen b/src/c_make.gen
+index 414dead..84c3030 100644
+--- a/src/c_make.gen
++++ b/src/c_make.gen
+@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
+ #### Do not redefine if (a) passed in on command line, or (b)
+ #### defined in an environment variable.
+
+-ifneq "$(origin CC)" "environment"
+-CC = cc
+-endif
+-
+-ifneq "$(origin CPPFLAGS)" "environment"
+-CPPFLAGS=
+-endif
+-
+-ifneq "$(origin CFLAGS)" "environment"
+-CFLAGS =
+-endif
+-
+-ifneq "$(origin CDEFS)" "environment"
+-CDEFS =
+-endif
+-
+-ifneq "$(origin CXX)" "environment"
+-CXX = g++
+-endif
+-
+-ifneq "$(origin CXXFLAGS)" "environment"
+-CXXFLAGS=
+-endif
+-
+-ifneq "$(origin CXXDEFS)" "environment"
+-CXXDEFS= -D__cplusplus
+-endif
+-
+-ifneq "$(origin AR)" "environment"
+-AR = ar
+-endif
+-
+-ifneq "$(origin ARFLAGS)" "environment"
+-ARFLAGS = rvs
+-endif
+-
+-ifneq "$(origin LDFLAGS)" "environment"
+-LDFLAGS =
+-endif
++CC ?= cc
++CXX ?= g++
++CXXFLAGS ?=
++CXXDEFS = -D__cplusplus
++AR ?= ar
++ARFLAGS ?= rvs
+
+ #### Delete default suffix rules
+ .SUFFIXES:
+@@ -359,13 +326,13 @@ $(PROGS):
+ cd $(LOCAL_OBJ); \
+ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ else \
+ cd $(LOCAL_OBJ); \
+ if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ fi ;
+
+diff --git a/src/c_make.glm b/src/c_make.glm
+index 0decc17..b82131c 100644
+--- a/src/c_make.glm
++++ b/src/c_make.glm
+@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen
+
+ SUBDIRS = Common ICM Glimmer Util
+
+-CFLAGS = -g -Wall
+-CXXFLAGS = -g -Wall
+-
+-LDFLAGS = -g -lm
++LIBS = -lm
+
+
+ #AS_BUILD_DIR =$(LOCAL_WORK)
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
new file mode 100644
index 000000000000..91498b116d12
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
@@ -0,0 +1,22 @@
+diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
+--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100
+@@ -2,12 +2,12 @@
+
+
+ all:
+- @ TGT=objs
+- @ $(dosubdirs)
+- @ TGT=libs
+- @ $(dosubdirs)
+- @ TGT=progs
+- @ $(dosubdirs)
++ @+ TGT=objs
++ @+ $(dosubdirs)
++ @+ TGT=libs
++ @+ $(dosubdirs)
++ @+ TGT=progs
++ @+ $(dosubdirs)
+
+
+ install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
new file mode 100644
index 000000000000..0a04fbef1dcc
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
@@ -0,0 +1,88 @@
+diff --git a/src/c_make.gen b/src/c_make.gen
+index 414dead..84c3030 100644
+--- a/src/c_make.gen
++++ b/src/c_make.gen
+@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
+ #### Do not redefine if (a) passed in on command line, or (b)
+ #### defined in an environment variable.
+
+-ifneq "$(origin CC)" "environment"
+-CC = cc
+-endif
+-
+-ifneq "$(origin CPPFLAGS)" "environment"
+-CPPFLAGS=
+-endif
+-
+-ifneq "$(origin CFLAGS)" "environment"
+-CFLAGS =
+-endif
+-
+-ifneq "$(origin CDEFS)" "environment"
+-CDEFS =
+-endif
+-
+-ifneq "$(origin CXX)" "environment"
+-CXX = g++
+-endif
+-
+-ifneq "$(origin CXXFLAGS)" "environment"
+-CXXFLAGS=
+-endif
+-
+-ifneq "$(origin CXXDEFS)" "environment"
+-CXXDEFS= -D__cplusplus
+-endif
+-
+-ifneq "$(origin AR)" "environment"
+-AR = ar
+-endif
+-
+-ifneq "$(origin ARFLAGS)" "environment"
+-ARFLAGS = rvs
+-endif
+-
+-ifneq "$(origin LDFLAGS)" "environment"
+-LDFLAGS =
+-endif
++CC ?= cc
++CXX ?= g++
++CXXFLAGS ?=
++CXXDEFS = -D__cplusplus
++AR ?= ar
++ARFLAGS ?= rvs
+
+ #### Delete default suffix rules
+ .SUFFIXES:
+@@ -359,13 +326,13 @@ $(PROGS):
+ cd $(LOCAL_OBJ); \
+ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ else \
+ cd $(LOCAL_OBJ); \
+ if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ fi ;
+
+diff --git a/src/c_make.glm b/src/c_make.glm
+index 0decc17..b82131c 100644
+--- a/src/c_make.glm
++++ b/src/c_make.glm
+@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen
+
+ SUBDIRS = Common ICM Glimmer Util
+
+-CFLAGS = -g -Wall
+-CXXFLAGS = -g -Wall
+-
+-LDFLAGS = -g -lm
++LIBS = -lm
+
+
+ #AS_BUILD_DIR =$(LOCAL_WORK)
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
new file mode 100644
index 000000000000..6eebc5610414
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
@@ -0,0 +1,196 @@
+diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
+--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200
+@@ -306,7 +306,7 @@
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+ long-orfs -n -t 1.15 genom.seq run1.longorfs
+- extract -t genom.seq run1.longorfs > run1.train
++ glimmer_extract -t genom.seq run1.longorfs > run1.train
+ build-icm -r run1.icm < run1.train
+ glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
+ \end{verbatim}\ESV
+@@ -330,9 +330,9 @@
+ \end{verbatim}\ESV
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+- extract -t genom.seq train.coords > run2.train
++ glimmer_extract -t genom.seq train.coords > run2.train
+ build-icm -r run2.icm < run2.train
+- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
++ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream
+ elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
+ set startuse = `start-codon-distrib -3 genom.seq train.coords`
+ glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
+@@ -358,11 +358,11 @@
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+ long-orfs -n -t 1.15 genom.seq run3.longorfs
+- extract -t genom.seq run3.longorfs > run3.train
++ glimmer_extract -t genom.seq run3.longorfs > run3.train
+ build-icm -r run3.icm < run3.train
+ glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
+ tail +2 run3.run1.predict > run3.coords
+- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
++ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream
+ elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
+ set startuse = `start-codon-distrib -3 genom.seq run3.coords`
+ glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
+@@ -1081,12 +1081,12 @@
+ \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
+ \eq
+
+-\subsubsection{\Pg{extract} Program}
++\subsubsection{\Pg{glimmer_extract} Program}
+ This program reads a genome sequence and a list of coordinates
+ for it and outputs a multi-fasta file of the regions specified
+ by the coordinates. Output goes to standard output.
+ \bq
+- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
++ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
+ \eq
+
+ \subsubsection{\Pg{multi-extract} Program}
+diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh
+--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12 21:46:35.000000000 +0200
++++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748 +0200
+@@ -50,7 +50,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh
+--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12 21:46:35.000000000 +0200
++++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25 22:40:18.450338748 +0200
+@@ -42,7 +42,7 @@
+ step1:
+ # Extract the training sequences from the genome file
+ echo "Step 1 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $coords > $tag.train
++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -66,7 +66,7 @@
+ # upstream of the start locations in $coords
+ echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh
+--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000 +0200
++++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748 +0200
+@@ -57,7 +57,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -103,7 +103,7 @@
+ # upstream of the start locations in $tag.coords
+ echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $tag.coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh
+--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177 +0200
+@@ -50,7 +50,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh
+--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177 +0200
+@@ -42,7 +42,7 @@
+ step1:
+ # Extract the training sequences from the genome file
+ echo "Step 1 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $coords > $tag.train
++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -66,7 +66,7 @@
+ # upstream of the start locations in $coords
+ echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh
+--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000 +0200
++++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177 +0200
+@@ -57,7 +57,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -103,7 +103,7 @@
+ # upstream of the start locations in $tag.coords
+ echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $tag.coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
+--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200
+@@ -8,7 +8,7 @@
+ SOURCES = $(UTIL_SRCS)
+ OBJECTS = $(UTIL_OBJS)
+
+-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \
++PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \
+ uncovered window-acgt
+
+ LIBRARIES =
+diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
+--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200
+@@ -297,7 +297,7 @@
+
+ {
+ fprintf (stderr,
+- "USAGE: extract [options] <sequence-file> <coords>\n"
++ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n"
+ "\n"
+ "Read fasta-format <sequence-file> and extract from it the\n"
+ "subsequences specified by <coords>. By default, <coords>\n"
+--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200
++++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200
+@@ -21,7 +21,7 @@
+
+ entropy-score: entropy-score.o libGLMcommon.a
+
+-extract: extract.o libGLMcommon.a
++glimmer_extract: extract.o libGLMcommon.a
+
+ multi-extract: multi-extract.o libGLMcommon.a
+
diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
new file mode 100644
index 000000000000..acc0eb98e18b
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit eutils toolchain-funcs
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/${PN}${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-glibc210.patch
+ "${FILESDIR}"/${P}-jobserver-fix.patch
+ "${FILESDIR}"/${P}-ldflags.patch
+ "${FILESDIR}"/${PN}-3.02b-rename_extract.patch
+)
+
+src_prepare() {
+ sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
+ # Fix Makefile to die on failure
+ sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
+ # GCC 4.3 include fix
+ sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die
+ epatch "${PATCHES[@]}"
+}
+
+src_compile() {
+ emake \
+ -C src \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ AR=$(tc-getAR) \
+ CXXFLAGS="${CXXFLAGS}" \
+ CFLAGS="${CFLAGS}" \
+ LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ rm bin/test || die
+ dobin bin/*
+
+ insinto /usr/share/${PN}
+ doins -r scripts
+
+ dodoc glim302notes.pdf
+}
diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
new file mode 100644
index 000000000000..0ebbbabe0c99
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit eutils toolchain-funcs
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
+SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh
+ sci-biology/elph"
+
+#S="${WORKDIR}/${PN}${PV}"
+S="${WORKDIR}/${PN}3.02"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-jobserver-fix.patch
+ "${FILESDIR}"/${P}-ldflags.patch
+ "${FILESDIR}"/${P}-rename_extract.patch
+)
+
+src_prepare() {
+ sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
+ # Fix Makefile to die on failure
+ sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
+ # GCC 4.3 include fix
+ sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die
+ #
+ sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die
+ sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die
+ sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die
+ sed -i "s/@ if/if/" src/c_make.gen || die
+ # avoid file collision on /usr/bin/extract #247394
+ epatch "${PATCHES[@]}"
+}
+
+src_compile() {
+ emake \
+ -C src \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ AR=$(tc-getAR) \
+ CXXFLAGS="${CXXFLAGS}" \
+ CFLAGS="${CFLAGS}" \
+ LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ rm bin/test || die
+ dobin bin/*
+
+ insinto /usr/share/${PN}
+ doins -r scripts
+
+ dodoc glim302notes.pdf
+}
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/glimmer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
new file mode 100644
index 000000000000..fd4e75d3fee9
--- /dev/null
+++ b/sci-biology/glimmerhmm/Manifest
@@ -0,0 +1 @@
+DIST GlimmerHMM-3.0.1.tar.gz 45475952 SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 WHIRLPOOL f2cc0f6cea083c223273dd59f9474a054c049b697fc122925d4f5820170ade67bfa76c6dd218ab10be5675fe0a2a2a9fa5172be540509770332cc5a1d6862ff7
diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
new file mode 100644
index 000000000000..949a4fe3e92d
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
@@ -0,0 +1,153 @@
+ sources/makefile | 15 +++++--------
+ train/makefile | 59 +++++++++++++++++++++++++++++++----------------------
+ 2 files changed, 40 insertions(+), 34 deletions(-)
+
+diff --git a/sources/makefile b/sources/makefile
+index f287d71..c560f48 100644
+--- a/sources/makefile
++++ b/sources/makefile
+@@ -2,25 +2,22 @@
+
+
+
+-CC=g++
+-CFLAGS=-g
+-
+ all: glimmerhmm
+
+ glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
+- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm
+
+ glimmerhmm.o: glimmerhmm.c
+- $(CC) $(CFLAGS) -c glimmerhmm.c
++ $(CXX) $(CXXFLAGS) -c glimmerhmm.c
+
+ graph.o: graph.c
+- $(CC) $(CFLAGS) -c graph.c
++ $(CXX) $(CXXFLAGS) -c graph.c
+
+ sites.o: sites.c
+- $(CC) $(CFLAGS) -c sites.c
++ $(CXX) $(CXXFLAGS) -c sites.c
+
+ tree_util_prob.o: tree_util_prob.c
+- $(CC) $(CFLAGS) -c tree_util_prob.c
++ $(CXX) $(CXXFLAGS) -c tree_util_prob.c
+
+ util.o: util.c
+- $(CC) $(CFLAGS) -c util.c
++ $(CXX) $(CXXFLAGS) -c util.c
+diff --git a/train/makefile b/train/makefile
+index 2383f18..d5a7107 100644
+--- a/train/makefile
++++ b/train/makefile
+@@ -2,9 +2,6 @@
+
+ # C compiler
+
+-C = gcc
+-CC = g++
+-CFLAGS = -O1 ${SEARCHDIRS}
+ #CFLAGS = -O3 -g -Wall
+ LIBS = -lm
+
+@@ -15,64 +12,76 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
+
+
+ misc.o: misc.c
+- ${C} ${CFLAGS} -c misc.c
++ $(CC) $(CFLAGS) -c misc.c
+
+ build-icm.o: build-icm.c
+- ${C} ${CFLAGS} -c build-icm.c
++ $(CC) $(CFLAGS) -c build-icm.c
+
+ build-icm: build-icm.o misc.o
+- $(C) -o $@ build-icm.o misc.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
+
+ build-icm-noframe.o: build-icm-noframe.c
+- ${C} ${CFLAGS} -c build-icm-noframe.c
++ $(CC) $(CFLAGS) -c build-icm-noframe.c
+
+ build-icm-noframe: build-icm-noframe.o misc.o
+- $(C) -o $@ build-icm-noframe.o misc.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
+
+ build1: build1.o
+- ${CC} build1.c -o build1 $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS)
+
+ build2: build2.o
+- ${CC} build2.c -o build2 $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS)
+
+ falsecomp: falsecomp.o
+- ${CC} falsecomp.c -o falsecomp $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS)
+
+ findsites: findsites.o
+- ${CC} findsites.c -o findsites $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS)
+
+ karlin: karlin.o
+- ${CC} karlin.c -o karlin $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS)
+
+ score: score.o
+- ${CC} score.c -o score $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS)
+
+ score2: score2.o
+- ${CC} score2.c -o score2 $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS)
+
+ scoreATG: scoreATG.o
+- ${CC} scoreATG.c -o scoreATG $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS)
+
+ scoreATG2: scoreATG2.o
+- ${CC} scoreATG2.c -o scoreATG2 $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS)
+
+ scoreSTOP: scoreSTOP.o
+- ${CC} scoreSTOP.c -o scoreSTOP $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS)
+
+ escoreSTOP2: scoreSTOP2.o
+- ${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS)
+
+-rfapp: erfapp.o
+- ${CC} erfapp.c -o erfapp $(LIBS)
++erfapp: erfapp.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
+
+ sites.o: sites.c
+- ${CC} ${CFLAGS} -c sites.c
++ $(CXX) $(CXXFLAGS) -c sites.c
++
++scoreATG.o: scoreATG.c
++ $(CXX) $(CXXFLAGS) -c scoreATG.c
++
++scoreSTOP.o: scoreSTOP.c
++ $(CXX) $(CXXFLAGS) -c scoreSTOP.c
++
++scoreSTOP2.o: scoreSTOP2.c
++ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c
++
++scoreATG2.o: scoreATG2.c
++ $(CXX) $(CXXFLAGS) -c scoreATG2.c
+
+ utils.o: utils.c
+- ${CC} ${CFLAGS} -c utils.c
++ $(CXX) $(CXXFLAGS) -c utils.c
+
+ splicescore.o: splicescore.c
+- ${CC} ${CFLAGS} -c splicescore.c
++ $(CXX) $(CXXFLAGS) -c splicescore.c
+
+ splicescore: splicescore.o sites.o utils.o
+- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
new file mode 100644
index 000000000000..bbddc6bdc8ad
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="A eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+src_unpack() {
+ unpack ${A}
+ mv GlimmerHMM ${P}
+}
+
+src_prepare() {
+ sed \
+ -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
+ -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
+ -i "${S}/train/trainGlimmerHMM" || die
+
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+ tc-export CC CXX
+}
+
+src_compile() {
+ emake -C "${S}/sources"
+ emake -C "${S}/train"
+}
+
+src_install() {
+ dobin sources/glimmerhmm train/trainGlimmerHMM
+
+ insinto /usr/share/${PN}/lib
+ doins train/*.pm
+ insinto /usr/share/${PN}/models
+ doins -r trained_dir/*
+ exeinto /usr/libexec/${PN}/training_utils
+ doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+ dodoc README.first train/readme.train
+}
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/glimmerhmm/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest
new file mode 100644
index 000000000000..b15b9200188f
--- /dev/null
+++ b/sci-biology/gmap/Manifest
@@ -0,0 +1,2 @@
+DIST gmap-gsnap-2011-10-07.tar.gz 3404351 SHA256 e508009592d5dd3442345dc5ce6fd9930366e008efa32e4c72dc243a495f3f20 SHA512 6546be4da41c45e41bdab71dcda69cbf172bc186ca64a2543461eb050f383641a13fea0cfcc6bb76b87cc4faa4c593944b029ee1ca2ba68dbaf7d939d0bf02e1 WHIRLPOOL 9f5cd62fb9cbb2cc73d6b971f29d8816e67e1b4b1b9906d8b06ddf99ffd9356bcdf19869066fb14ca5d3ad93a3b70527d05237be2f438da4db86898103bd2bf2
+DIST gmap-gsnap-2012-07-20.tar.gz 3623122 SHA256 4cd0c0a313cb7a35b8c7afd45b545e6062b343739f9ef522a09001d448aeb5ec SHA512 bbc22509fc63814a102f96ce0da6a1119c78de7fc2fc4fe17cc4d97881313a77818eaedc51bb6d4ce2426560925fe5ffa121acf972d7b3b097e8d3d65efb7b95 WHIRLPOOL 7318377e4cf80db5c5a9495bf68653fbc48051d6fa5748ed796e18888b6e20215d2714b753358fb4cc97aa9c8e441d53ef616ded6ee0923fe78312e78ee91e82
diff --git a/sci-biology/gmap/gmap-2011.10.07.ebuild b/sci-biology/gmap/gmap-2011.10.07.ebuild
new file mode 100644
index 000000000000..fb20296c2654
--- /dev/null
+++ b/sci-biology/gmap/gmap-2011.10.07.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+MY_PV=${PV//./-}
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://www.gene.com/share/gmap/"
+SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+IUSE="+samtools +goby"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="samtools? ( sci-biology/samtools )
+ goby? ( sci-biology/goby-cpp )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/gmap-${MY_PV}"
+
+src_configure() {
+ econf $(use_with samtools) \
+ $(use_with goby goby /usr)
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS ChangeLog README
+}
+
+src_test() {
+ emake check || die
+}
diff --git a/sci-biology/gmap/gmap-2012.07.20.ebuild b/sci-biology/gmap/gmap-2012.07.20.ebuild
new file mode 100644
index 000000000000..cd20c09b57f8
--- /dev/null
+++ b/sci-biology/gmap/gmap-2012.07.20.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+MY_PV=${PV//./-}
+
+DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
+HOMEPAGE="http://research-pub.gene.com/gmap/"
+SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
+
+LICENSE="gmap"
+SLOT="0"
+IUSE="+samtools +goby"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="samtools? ( sci-biology/samtools )
+ goby? ( sci-biology/goby-cpp )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/gmap-${MY_PV}"
+
+src_configure() {
+ econf $(use_with samtools) \
+ $(use_with goby goby /usr)
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS ChangeLog README
+}
+
+src_test() {
+ emake check || die
+}
diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml
new file mode 100644
index 000000000000..7d62e2f44e07
--- /dev/null
+++ b/sci-biology/gmap/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="samtools">Enable support for samtools</flag>
+ <flag name="goby">Enable support for goby</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest
new file mode 100644
index 000000000000..b9ab55a817cd
--- /dev/null
+++ b/sci-biology/goby-cpp/Manifest
@@ -0,0 +1,3 @@
+DIST goby_1.9.7.3-cpp.zip 127215 SHA256 8493daa7c850732c6c48d4512bd26b7eec411a729b39d9861a4a6aae08faa674
+DIST goby_1.9.8.1-cpp.zip 134904 SHA256 2f1bd87f2870af178f34a8e7c11819aa9e42f35e20f1985d2ceb054f452e2a97 SHA512 d31cd7f0be19074bfe8da74d9f2510f0e0f15fe6c485bbed8520052468d2cd2f1bc5fcad8b0d6a1586f5acde73db326059f45994ecfbb5fb6c09692d8e155190 WHIRLPOOL 6ce51c46f8802d31068f510f6da13b2920086eafdae24506830b42d79e48eb6ed9cac48a96090a81964daebf4a0c8f21c490ca3b0af2f589ac57647bde1be79f
+DIST goby_2.0.1-cpp.zip 177718 SHA256 5ec57b833cb1a0f53e975112d1c360b14a9b17cfff3fb0ad77dd70672c1881db SHA512 992bd10d5538dec1478820f26151dd311f4de13e7947b49f0b06d6cbdd4b71deeb3aa8a4c6a598fb92fbcb9cbf4ff97bf81205c9389d4a0da4443317e48aea9f WHIRLPOOL ab94cf674703917b6f0cde812d0fbcd94e18fb6055b30d6a1eefa1e4cb5b76bbe18c67388c66e25e87e522df9a9946b0eae5a164428abe874a382f5bc39a13d0
diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto
new file mode 100644
index 000000000000..fe7f56647644
--- /dev/null
+++ b/sci-biology/goby-cpp/files/Alignments.proto
@@ -0,0 +1,597 @@
+package goby;
+
+option java_package = "edu.cornell.med.icb.goby.alignments";
+
+option optimize_for = SPEED;
+
+/*
+ This message is written to 'basename'.entries as a very large chunked collection.
+*/
+message AlignmentCollection {
+ repeated AlignmentEntry alignment_entries = 1;
+}
+
+
+message AlignmentEntry {
+ /* Multiplicity of this entry. The number of times this alignment entry would be repeated exactly the same if
+ query redundancy had not been removed by read factorization.
+ */
+ optional uint32 multiplicity = 7;
+
+ /*
+ Compressed stream of data. Removed since Goby 2.0 supports chunk codecs. Do not reuse field index 23
+ optional bytes compressed_data = 23;
+ */
+
+ /* An integer that uniquely identifies the query (a short read) in a set of alignment runs. When several
+ alignment runs are made with the same set of query sequences, equality of query index means that the query
+ sequences were the same. (Comparing integers for equality is much faster than comparing strings.)
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 query_index = 1;
+ /* An integer that uniquely identifies the target (e.g., a chromosome) in a set of alignment runs. When several
+ alignment runs are made with the same set of target sequences, equality of target index means that the target
+ sequence was the same across the runs. (Comparing integers for equality is much faster than comparing strings.)
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 target_index = 2;
+ /*
+ The position on the target of the start of the alignment between the query and the target.
+ In the following example, position is 3 because the third base of the query 'C' was aligned with
+ position 3 of the reference (two read bases were soft clipped: "ct"). This example shows that the
+ alignment can start at a mismatch if it was so constructed by the aligner.
+
+ 0123456789
+ AAAAGTCAAA target
+ ctCGTC query
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 position = 3;
+
+ /*
+ True when the query matches the target on the reverse strand
+ */
+ optional bool matching_reverse_strand = 6;
+
+ /*
+ The position on the query where the alignment starts. This value is different from zero
+ when some bases/residues of the query could not be aligned with the target.
+ TODO: Rename this to left_trim. Add a right_trim property.
+ */
+ optional uint32 query_position = 5;
+
+ /*
+ The score of the alignment, where larger scores indicate better matches between the query and the target.
+ If an aligner outputs only the number of mismatches between query and target, the score is taken to be
+ -(#mismatches(query,target)).
+ */
+ optional float score = 4;
+
+ /*
+ Number of bases/residues that differ in the alignment between query and target sequences.
+ */
+ optional uint32 number_of_mismatches = 8;
+
+ /*
+ Cumulative number of insertions and/or deletions present in the alignment.
+ */
+ optional uint32 number_of_indels = 9;
+
+ /*
+ Number of bases that have been aligned for the query. Please note that query_aligned_length must be
+ less or equal to query_length.
+ */
+ optional uint32 query_aligned_length = 11;
+
+ /*
+ Number of bases that have been aligned for the target.
+ */
+ optional uint32 target_aligned_length = 12;
+
+ repeated SequenceVariation sequence_variations = 13;
+
+ /*
+ Length of the query sequence.
+ */
+ optional uint32 query_length = 10;
+ /*
+ Mapping Quality (phred-scaled posterior probability that the mapping
+ position of this read is incorrect). Please note that different aligners
+ may estimate mapping quality with different approaches, resulting in aligner
+ specific differences in the distribution of mapping quality. It is recommended
+ to condition mapping quality on the aligner that produced the specific alignment
+ being processed. See aligner name and version in the header.
+ Note that the following description is preliminary. A clear specification is
+ needed:
+ The mapping quality should be proportional to the
+ log of the probability that the given mapping is the "correct" one.
+ So if there are five equally good mappings of a read to the genome,
+ the probability of each would be 0.2, and the mapping quality would be
+ something like -10*log10(1-0.2) = 1. If a mapping is highly likely,
+ say a 1e-4 of it being wrong, then the mapping quality would be
+ -10*log10(1e-4) = 40.
+ */
+ optional int32 mapping_quality = 14;
+
+ /*
+ If this read was aligned with a pair, the flags for the pair alignment (based on SAM):
+ 000000001 paired
+ 000000010 properly paired
+ 000000100 read unmapped
+ 000001000 mate unmapped
+ 000010000 read reverse strand
+ 000100000 mate reverse strand
+ 001000000 first in pair
+ 010000000 second in pair
+ 100000000 not primary alignment
+ */
+ optional uint32 pair_flags = 15;
+
+ /*
+ If there is an alignment entry for the paired read (the paired read was mapped), a link to the entry is given.
+ */
+ optional RelatedAlignmentEntry pair_alignment_link = 16;
+
+ /* Index of the read fragment from which this alignment was obtained. */
+ optional uint32 fragment_index = 17;
+
+ /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
+ alignment entries, one for each matching part of the read, and link these entries with
+ spliced_alignment_links. The field spliced_forward_alignment_link points to the next
+ AlignmentEntry in the chain of spliced alignments.
+ */
+ optional RelatedAlignmentEntry spliced_forward_alignment_link = 18;
+
+ /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
+ alignment entries, one for each matching part of the read, and link these entries with
+ spliced_alignment_links. The field spliced_backward_alignment_link points to the previous
+ AlignmentEntry in the chain of spliced alignments.
+ */
+ optional RelatedAlignmentEntry spliced_backward_alignment_link = 22;
+
+ /*
+ If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two alignment entries, one for each
+ matching part of the read, and flag describes the spliced_alignment_link with these
+ binary flags:
+ 000000001 normal
+ 000000010 novel
+ */
+ optional uint32 spliced_flags = 19;
+
+ /* The size of the insert used when making the sequence library. This is the total size of the DNA
+ fragment to sequence, without the adapters. This is not the length of sequence that separates the reads.
+ See http://seqanswers.com/forums/showthread.php?t=8730 for details. Insert size is inferred for each pair
+ of reads by the aligner and is recorded here if was estimated (i.e., for paired-end reads).
+ */
+ optional sint32 insert_size = 20;
+
+ /*
+ The sample index. Uniquely identifies the aligned sample this read was read from. Storing the sample index in the
+ alignment entry makes it possible to concat alignments from different origins and track what sample originally
+ contained each entry.
+ */
+ optional uint32 sample_index = 21;
+ /*
+ The total number of times the query index associated with this entry occurs across the entire alignment file.
+
+ This field is used to purge queryIndex->smallIndex associations after all instances of a queryindex have
+ been seen (see QueryIndexPermutation class). When each entry has a value for this field, the header field
+ query_index_occurrences is true.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 query_index_occurrences = 25;
+ /*
+ The total number of times the read matches the reference across the entire alignment file. This differs from
+ query_index_occurrences because reads that are matching through splice and pair links count as one for ambiguity.
+ The field can be used to filter by ambiguity-threshold on the fly after an alignment has been done (to restrict
+ entries to more smaller thresholds). When each entry has a value for this field, the header field
+ ambiguity_stored_in_entries is true.
+
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 ambiguity = 27;
+ /*
+ List of BAM attributes, if the alignment was imported from BAM. The attributes are stored in exactly the format
+ allowed for BAM. For instance, X0:i:9 X1:i:1 MD:Z:68 RG:Z:SRR084825 will be stored as four strings:
+ "X0:i:9", "X1:i:1", "MD:Z:68", "RG:Z:SRR084825". Note that sam-to-compact will interpret some BAM attributes
+ and populate goby native fields. Such tags do not appear in bam_attributes, and are instead re-generated from
+ the corresponding goby native fields.
+ Since Goby 2.0.
+ */
+ repeated string bam_attributes = 50;
+ /*
+ Quality scores for all bases of the read.
+ Since Goby 2.0.
+ */
+ optional bytes read_quality_scores = 55;
+
+ /*
+ Origin index. An integer that references a ReadOriginInfo message in the alignment header and
+ makes it possible to track the origin of the read (especially useful after several alignments
+ have been merged/concatenated).
+ (Since Goby 2.0).
+ */
+ optional uint32 read_origin_index = 26;
+ /*
+ Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
+ erroneous bases, or bases that belong to a different part of the reference genome. Left clipped bases are
+ stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
+ the reference base. For instance "A=G" for three soft-clipped bases, the middle one matching the genome at
+ this position. The number of bases in softClippedBasesLeft is exactly equal to queryPosition.
+ */
+ optional string softClippedBasesLeft = 30;
+ /*
+ Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
+ erroneous bases, or bases that belong to a different part of the reference genome. Right clipped bases are
+ stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
+ the reference base. The number of bases in softClippedBasesRight is exactly equal
+ to queryLength - queryAlignedLength - queryPosition.
+ */
+ optional string softClippedBasesRight = 31;
+
+ /*
+ Quality scores for bases in softClippedBasesLeft. Stored in Phred Units.
+ */
+ optional bytes softClippedQualityLeft = 32;
+ /*
+ Quality scores for bases in softClippedBasesRight. Stored in Phred Units.
+ */
+ optional bytes softClippedQualityRight = 33;
+ /*
+ Sequence for a read placed near this entry, but unmapped to the reference sequence. For instance, used to record
+ the sequence of a mate that did not map to the reference. We know that the mate maps in the proximity of this entry
+ (it is placed) but are unable to map it to a specific genomic position. The sequence is always given as obtained
+ from the reads file.
+ */
+ optional string placedUnmappedSequence=40;
+ /*
+ Quality scores for a read placed near this entry. Phred units.
+ */
+ optional bytes placedUnmappedQuality=41;
+
+ /*
+ Read name. In SAM/BAM this is referred to as QNAME. Paired and segmented reads will have the same Read name.
+ */
+ optional string readName=42;
+}
+
+/* A link to another alignment entry. This message type is used to represent relations
+ between alignments, such as the relation between the two read fragments in a paired-end protocol,
+ or the relation between parts of reads that align through an exon exon junction and map in
+ different locations of the genome.
+ */
+message RelatedAlignmentEntry {
+ /* Target index of the location where the other alignment entry is mapped.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 target_index = 1;
+
+ /* Position on the reference where the other alignment entry is mapped. *
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 position = 2;
+
+ /* Index of the fragment for the related alignment entry. This index
+ makes it possible to identify which of the read fragments mapped to the given
+ location is related to the source alignment entry.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 fragment_index = 3;
+
+ optional uint32 optimized_index=50;
+}
+
+/*
+ Represents sequence variations between the query and the reference sequences. Many variations can be represented.
+ For instance, an insertion at position 5 in the reference would be represented as from="A", to="" position=5.
+ A mutation T->G at position 6 would be rendered as from="T", to="G" position=6. Padded alignments (see SAM description)
+ can be described by a combination of pair-wise alignments, where the gap character '-' is used to indicate that no
+ base exists in the sequence considered for the alignment position, for instance:
+
+ - Padding example:
+
+ 123 (<-positions)
+ref A-C
+ A-T [from="-" to="" position=2] [from="C" to="T" position=3]
+ ACT [from="" to="C" position=2] [from="C" to="T" position=3]
+ A-T [from="-" to="" position=2] [from="C" to="T" position=3]
+
+ - Mutation example:
+ 123 (<-positions)
+ref ATT
+ ACT [from="T" to="C" position=2]
+
+ -- Example of deletion in a read:
+ 123 (<-positions)
+ref ATT
+ A-T [from="T" to="-" position=2]
+
+ -- Example of insertion of two base pairs in a read:
+ 12345 (<-positions)
+ref A--TT
+ ACCTT [from="" to="CC" position=2]
+
+ */
+message SequenceVariation {
+ /* The reference bases. Can include one or more gap characters '-', to indicate that the reference sequence has
+ no base at this alignment position.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional string from = 2;
+ /* The read bases that differ from the reference sequence. Can include one or more gap characters '-', to indicate
+ that the query sequence has no base at this alignment position.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional string to = 1;
+ /*
+ The position of the variation on the read, as if the read always matched on the forward strand.
+ Adding position to the index where the reference starts aligning the read yields the position of the variation
+ in reference/target sequence space. Since position starts at one the resulting position will also be one based.
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 position = 3;
+ /*
+ The position of the variation, starting from the beginning of the aligned read (position 1), and up to the length
+ of the read (inclusive). Use this index if you need to know how far the variation is observed from the beginning
+ of the sequenced read. When the read has an insertion, this index records the position immediately before the base
+ where the bases are inserted (these bases are in the to field).
+ When the read has a deletion, read_index records the position in the read after which the bases that would align
+ in the reference are missing (these bases are in the from field).
+ This field is required (enforced by semantic validation in Goby 2.0+).
+ */
+ optional uint32 read_index = 5;
+
+ /**
+ The read base quality scores for those bases that are given in the to field. This field
+ is populated when the reads used to perform the search include quality scores, and when
+ the alignment parser can extract the information from the aligner's output.
+ (this option is currently not implemented in Goby.)
+ */
+ optional bytes to_quality = 4;
+
+}
+/*
+ This message is written to 'basename'.header
+*/
+
+message AlignmentHeader {
+ /*
+ The smallest possible query index in this alignment. Data stored as an array where
+ queryIndex is the array index will be stored with only the elements in the inclusive
+ range [smallestSplitQueryIndex largestSplitQueryIndex]
+ Such data structures include queryLength and some arrays in the TooManyHits data
+ structure.
+ */
+ optional uint32 smallest_split_query_index = 9;
+ /*
+ The largest possible query index in this alignment. Data stored as an array where
+ queryIndex is the array index will be stored with only the elements in the inclusive
+ range [smallestSplitQueryIndex largestSplitQueryIndex]
+ Such data structures include queryLength and some arrays in the TooManyHits data
+ structure.
+ */
+ optional uint32 largest_split_query_index = 11;
+
+ /* Mapping from query identifier name to query index (as used in alignment entries).
+ */
+ optional IdentifierMapping query_name_mapping = 1;
+
+ /* Mapping from target identifier name to target index (as used in alignment entries).
+ */
+ optional IdentifierMapping target_name_mapping = 2;
+
+ /*
+ The number of query sequences
+ */
+ optional uint32 number_of_queries = 5;
+ /*
+ The number of target sequences
+ */
+ optional uint32 number_of_targets = 6;
+ /*
+ The number of reads that were aligned to the reference and are represented in this alignment archive.
+ */
+ optional uint32 number_of_aligned_reads = 7;
+
+ /*
+ Length of the query sequences. One number per query, in the order of increasing query index.
+ This information has been moved to the individual alignment entries.
+ */
+ repeated uint32 query_length = 3 [deprecated = true];
+ /*
+ If query length is constant across all the queries, this field contains the constant length.
+ In such cases, query_length will be empty.
+ */
+ optional uint32 constant_query_length = 10;
+
+ /*
+ Length of the target sequences. One number per target, in the order of increasing target index.
+ The target indexes must be 0..(number of targets - 1).
+ */
+ repeated uint32 target_length = 8;
+ /*
+ Indicates whether this alignment is sorted by position. True: the alignment entries occur in sorted
+ order, such that entry a occurs before entry b if a.targetIndex< b.targetIndex or, when entries
+ have the same target, when a.position < b.position.
+ */
+ optional bool sorted = 13;
+
+ /*
+ Indicates whether this alignment is indexed by position. When this attribute is true, a file called
+ 'basename'.index exists that contains the AlignmentIndex message (GZip compressed).
+ */
+ optional bool indexed = 14;
+ /*
+ True when query lengths are stored in alignment entries (Goby 1.7+).
+ */
+ optional bool query_lengths_stored_in_entries = 15;
+ /*
+ Name of the aligner that produced this alignment.
+ */
+ optional string aligner_name = 17;
+ /*
+ Version number for the aligner implementation that produced this alignment.
+ */
+ optional string aligner_version = 18;
+ /*
+ The version of Goby that created this alignment file.
+ */
+ optional string version = 25;
+
+ /*
+ Sample basenames, in the order of increasing sampleIndex, starting with sampleIndex=0.
+ */
+
+ repeated string sample_basename = 30;
+
+ /*
+ This field is true when the query indices of alignment entries were permuted to smaller indices. Only sorted
+ alignments can have query_indices_were_permuted=true. When the field is true, and you need to retrieve the
+ original query-index of an alignment (because you want to retrieve the specific read(s) from a read file for
+ instance), you will need the information in the permutation file (extension basename.perm) and transform back
+ each small index of interest to the original query index.
+ */
+ optional bool query_indices_were_permuted = 26;
+ /*
+ This field is true when entries in the alignment .entries file all have the query_index_occurrences field populated
+ (Since Goby 2.0).
+ */
+ optional bool query_index_occurrences = 35;
+
+ /*
+ This field is true when entries in the alignment .entries file all have the ambiguity field populated
+ (Since Goby 2.0).
+ */
+ optional bool ambiguity_stored_in_entries = 36;
+ /*
+ This field is true when entries in the alignment .entries file all have the read_quality_score field populated.
+ (Since Goby 2.0).
+ */
+ optional bool all_read_quality_scores = 40;
+ /*
+ A description of the origin of sets of reads. Serves a similar function to BAM read groups, but more flexible and
+ efficient. Instead of storing strings, we use integers in the entries.
+ Alignemnt entries will link to a specific ReadOriginInfo with the origin_index field.
+ (Since Goby 2.0).
+ */
+ repeated ReadOriginInfo read_origin = 27;
+}
+
+message IdentifierMapping {
+ repeated IdentifierInfo mappings = 1;
+}
+
+message IdentifierInfo {
+ required string name = 1;
+ required uint32 index = 2;
+}
+
+
+/*
+ A description of the origin of sets of reads. Stored in the Goby alignment header and linked
+ from alignment entries. Goby makes it possible to adapt origin equivalence rules on the fly
+ efficiently. To do this, it is sufficient to read the header of the alignment, decide which
+ ReadOriginInfo instances are equivalent (e.g., by looking at sample, platform, library, or
+ other fields in the message), then construct a function e(a):int. This function takes
+ one originIndex parameter and returns another integer that maps to an equivalent class. The
+ equivalence class can be used to estimate error models for entries that belong to each class,
+ for instance.
+ (Since Goby 2.0).
+ */
+message ReadOriginInfo {
+ /*
+ Origin index. An integer that links alignment entries to their origin information.
+ */
+ required uint32 origin_index = 1;
+ /*
+ Identifier that describes the origin of the reads. This field is compatible with the ID/platform field of BAM read
+ groups. Free text.
+ */
+ required string origin_id = 2;
+ /*
+ The sample from which the reads were sequenced. This field is compatible with the SM/sample field of BAM read
+ groups. Free text.
+ */
+ optional string sample = 4;
+ /*
+ The platform on which the reads were sequenced. This field is compatible with the PL/platform field of BAM read
+ groups. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.
+ */
+ optional string platform = 5;
+ /*
+ The library from which the reads were sequenced. This field is compatible with the LB/library field of BAM read
+ groups. Free text.
+ */
+ optional string library = 8;
+ /*
+ The platform unit on which the reads were sequenced. This field for compatibility with samtools.
+ */
+ optional string platform_unit = 12;
+ /*
+ The date the reads were sequenced. Useful to identify batch effects, in the format dd:MMM:yyyy.
+ The month is Jan, Feb, etc. to avoid all confusion with days when day<=12.
+ */
+ optional string run_date = 6;
+}
+
+/*
+ This message is written to 'basename'.tmh
+*/
+
+message AlignmentTooManyHits {
+ /*
+ The threshold used by the aligner to determine that a query is ambiguous and should be dropped.
+ Referred to as parameter k below.
+ */
+ required uint32 aligner_threshold = 2;
+ /*
+ The hits that are assigned to several (>k) reference location.
+ */
+ repeated AmbiguousLocation hits = 1;
+
+}
+
+message AmbiguousLocation {
+ /*
+ The index of the query that matched too many times.
+ */
+ required uint32 query_index = 1;
+ /*
+ The number of hits that triggered membership in the too many hits list. The query may hit more
+ locations than reported here, since some alignment tools will just drop queries that match above
+ a threshold and stop counting. This number can be >=k.
+ */
+ required uint32 at_least_number_of_hits = 2;
+ /**
+The length of the part of the query sequence that could be matched to the target (also called depth).
+May be less than the length of the query sequence, in which case the match was not perfect. When merging
+alignments produced by searching different reference sequences, consider only at_least_number_of_hits
+from alignments that have exactly the longer depth for the query. */
+ optional uint32 length_of_match = 3;
+}
+
+/*
+ This message is written to 'basename'.index
+ */
+message AlignmentIndex {
+ /*
+ Stores one element by target sequence. Each element is the cumulative target length for the target
+ stored at index i. Assume there are four target sequences, with lengths {10, 12, 15, 34}. The field
+ targetPositionOffsets will contain: {0,10,22,37}. Such offsets can be used to calculate the absolute
+ position of a genomic location. Given targetIndex and positionOnReference, the absolute location
+ is defined as targetPositionOffsets[targetIndex]+positionOnReference.
+ */
+ repeated uint32 target_position_offsets = 1 [packed = true];
+ /*
+ The byte offsets into the compressed entries file. Byte offsets are matched with absolute position
+ by index. There should be as many elements in offsets as there are in absolutePosition
+ where chunks start which represent entries whose absolute positions are less than
+ */
+ repeated uint64 offsets = 2 [packed = true];
+ /*
+ The absolute positions of the first entry in the chunk that immediately start at offset. One element
+ per chunk in the 'basename'.entries file.
+ */
+ repeated uint64 absolute_positions = 3 [packed = true];
+
+}
diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto
new file mode 100644
index 000000000000..32c1244a3eb3
--- /dev/null
+++ b/sci-biology/goby-cpp/files/Reads.proto
@@ -0,0 +1,96 @@
+package goby;
+
+option java_package = "edu.cornell.med.icb.goby.reads";
+option optimize_for = SPEED;
+
+message ReadCollection {
+ repeated ReadEntry reads = 1;
+}
+
+message ReadEntry {
+ /*
+ Index of a read.
+ */
+ required uint32 read_index = 1;
+ /*
+ Index of the barcode, if any.
+ */
+ optional uint32 barcode_index = 10;
+ /*
+ Read identifier/name may be present.
+ */
+ optional string read_identifier = 23;
+ /*
+ Additional description about the read (from Fasta/Q format).
+ */
+ optional string description = 22;
+ /*
+ Length of the sequence.
+ */
+ required uint32 read_length = 2;
+ /*
+ Sequence, encoded as ascii characters stored in single bytes.
+ */
+ optional bytes sequence = 3;
+ /*
+ The second sequence in a pair. Stored the same way as the sequence attribute.
+ */
+ optional bytes sequence_pair = 5;
+ /*
+ Length of the second sequence in a pair.
+ */
+ optional uint32 read_length_pair = 6;
+ /*
+ Quality scores in Phred units, stored as single bytes (0-255).
+ */
+ optional bytes quality_scores = 4;
+ /*
+ Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute.
+ */
+ optional bytes quality_scores_pair = 7;
+ /*
+ Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are
+ content compressed with the codec.
+ */
+ optional bytes compressed_data = 8;
+ /*
+ Stores meta-data about the reads. Typically meta-data is stored in the very first read of a
+ read collection, with the understanding that the meta-data applies to all the reads in the
+ collection. Meta-data can be used to store information about when the sample was sequenced,
+ or other information of interest. The key-value pair format is sufficiently flexible to
+ accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined
+ keys so that automated tools can use metadata in relatively standard way. Please note that
+ some keys provide a format for the value. This format should also be followed to garantee
+ that meta data can be used computationally in fully automatic manner.
+
+ key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run
+ was initiated on the instrument. Can be used to detect batch effect in a large set of samples.
+ key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined.
+ Illumina GaIIx
+ Illumina HiSeq 1000
+ Illumina HiSeq 2000
+ Helicos Heliscope
+ LifeTech 5500 SOLiD
+ LifeTech 5500xl SOLiD
+ Roche 454 GS FLX Ti
+
+ key="organism" value="species name"
+ Since Goby 1.9.1
+ */
+ repeated MetaData meta_data = 25;
+
+}
+/*
+ A message to store a key/value pair and represent metadata about reads.
+ Since Goby 1.9.1
+ */
+message MetaData {
+ /*
+ Provides the key. See examples in the documentation of meta_data for ReadEntry.
+ */
+ required string key=1;
+ /*
+ Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry.
+ */
+ required string value=2;
+}
diff --git a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
new file mode 100644
index 000000000000..415785466af7
--- /dev/null
+++ b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
@@ -0,0 +1,16 @@
+ src/Makefile.am | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1033382..33ca906 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -84,7 +84,7 @@ GobyReadsStats_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_D
+ GobyReadsStats_SOURCES = \
+ GobyReadsStats.cc
+
+-GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
++GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} -lz
+ GobyFastaToCompact_SOURCES = \
+ GobyFastaToCompact.cc
+
diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild
new file mode 100644
index 000000000000..1b15aaac3ac6
--- /dev/null
+++ b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools
+
+DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=dev-libs/protobuf-2.4.1
+ >=dev-libs/libpcre-8.12"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/goby_${PV}/cpp"
+
+src_prepare() {
+ eautoreconf
+}
diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild
new file mode 100644
index 000000000000..c74f57306255
--- /dev/null
+++ b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools
+
+DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=dev-libs/protobuf-2.4.1
+ >=dev-libs/libpcre-8.12"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/goby_${PV}/cpp"
+
+src_prepare() {
+ eautoreconf
+}
diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
new file mode 100644
index 000000000000..2cadda103999
--- /dev/null
+++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ >=dev-libs/protobuf-2.4.1
+ >=dev-libs/libpcre-8.12"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PV}/cpp"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-underlinking.patch
+)
+
+src_prepare() {
+ sed \
+ -e '/BUILD_TIMESTAMP/s:\(goby/timestamp.h\):$(top_srcdir)/src/\1:g' \
+ -i src/Makefile.am || die
+
+ pushd src/goby > /dev/null || die
+ cp "${FILESDIR}"/*.proto . || die
+ protoc --cpp_out=. *.proto || die
+ popd > /dev/null || die
+
+ autotools-utils_src_prepare
+}
diff --git a/sci-biology/goby-cpp/metadata.xml b/sci-biology/goby-cpp/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/goby-cpp/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest
new file mode 100644
index 000000000000..9e3b65fbcbaa
--- /dev/null
+++ b/sci-biology/goby/Manifest
@@ -0,0 +1,4 @@
+DIST goby_1.9.7.3-deps.zip 19959489 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a
+DIST goby_1.9.7.3-src.zip 15642000 SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24
+DIST goby_1.9.8.1-deps.zip 20820943 SHA256 eb11916408a7978a1e90967783b8167b96c6d0dd60ae58cf1dab915a519d1bbb
+DIST goby_1.9.8.1-src.zip 15748880 SHA256 e2489a815a38bd10b1ec59b4e262a023f97994d9953f97bcc6571cadd05919c3
diff --git a/sci-biology/goby/goby-1.9.7.3.ebuild b/sci-biology/goby/goby-1.9.7.3.ebuild
new file mode 100644
index 000000000000..20622d49ffa7
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.7.3.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+ http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+ dev-java/commons-lang:2.1
+ dev-java/commons-io:1
+ dev-libs/protobuf[java]
+ dev-java/fastutil:5.0
+ dev-java/log4j
+ dev-java/jsap
+ dev-java/commons-configuration
+ dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}
+ cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i '/sge/ d' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar goby*.jar
+ java-pkg_dolauncher goby --jar goby.jar
+
+ insinto /usr/share/${PN}
+ doins -r python
+ dodoc CHANGES.txt
+}
diff --git a/sci-biology/goby/goby-1.9.8.1.ebuild b/sci-biology/goby/goby-1.9.8.1.ebuild
new file mode 100644
index 000000000000..5039b96941b3
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+ http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+ dev-java/commons-lang:2.1
+ dev-java/commons-io:1
+ dev-libs/protobuf[java]
+ dev-java/fastutil:5.0
+ dev-java/log4j
+ dev-java/jsap
+ dev-java/commons-configuration
+ dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}
+ cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i '/sge/ d' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar goby*.jar
+ java-pkg_dolauncher goby --jar goby.jar
+
+ insinto /usr/share/${PN}
+ doins -r python
+ dodoc CHANGES.txt
+}
diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml
new file mode 100644
index 000000000000..3bc02ac6b32e
--- /dev/null
+++ b/sci-biology/goby/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="cpp">Compile C/C++ API</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
new file mode 100644
index 000000000000..4ab0094769a2
--- /dev/null
+++ b/sci-biology/hmmer/Manifest
@@ -0,0 +1,2 @@
+DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4
+DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83
diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
new file mode 100644
index 000000000000..983827b0bd46
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
@@ -0,0 +1,23 @@
+--- easel/Makefile.in
++++ easel/Makefile.in
+@@ -26,8 +26,7 @@
+ LDFLAGS = @LDFLAGS@
+ SIMDFLAGS= @SIMD_CFLAGS@
+ CPPFLAGS = @CPPFLAGS@
+-LIBGSL = @LIBGSL@
+-LIBS = @LIBS@ @PTHREAD_LIBS@
++LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@
+
+ # Other tools
+ #
+@@ -252,8 +251,8 @@
+ else \
+ DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+ fi;\
+- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\
+- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm
++ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\
++ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+
+
+ # install: installs libeasel.a in ${libdir}/
diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch
new file mode 100644
index 000000000000..19d38c8e32ed
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch
@@ -0,0 +1,132 @@
+ easel/devkit/autodoc | 4 ++--
+ easel/devkit/esl-dependencies | 4 ++--
+ easel/devkit/sqc | 7 +++----
+ easel/testsuite/coverage_report.pl | 4 ++--
+ easel/testsuite/driver_report.pl | 4 ++--
+ easel/testsuite/valgrind_report.pl | 4 ++--
+ profmark/rocplot.pl | 4 ++--
+ 7 files changed, 15 insertions(+), 16 deletions(-)
+
+diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
+index 16bda4d..f5c5efc 100755
+--- a/easel/devkit/autodoc
++++ b/easel/devkit/autodoc
+@@ -49,8 +49,8 @@
+ #
+ # SRE, Tue Nov 30 19:43:47 2004
+
+-require "getopts.pl";
+-&Getopts('n:t');
++use Getopt::Std;
++getopts('n:t');
+ $cfile = shift;
+
+ if ($opt_t) { $show_api_table = 1; }
+diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
+index a4dc126..b61fa7a 100755
+--- a/easel/devkit/esl-dependencies
++++ b/easel/devkit/esl-dependencies
+@@ -13,8 +13,8 @@
+ # SRE, Mon Jun 11 11:15:31 2007
+ # SVN $Id$
+
+-require "getopts.pl"
+-&Getopts('1afr');
++use Getopt::Std;
++getopts('1afr');
+
+ if ($opt_1) { $show_summary_table = 1; }
+ if ($opt_a) { $list_augfiles = 1; }
+diff --git a/easel/devkit/sqc b/easel/devkit/sqc
+index af3adf6..0cdb458 100755
+--- a/easel/devkit/sqc
++++ b/easel/devkit/sqc
+@@ -205,12 +205,11 @@
+ # SRE, Tue Aug 6 11:16:39 2002
+ # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
+
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+
+ # Parse our command line
+ #
+-&Getopts('v');
++getopts('v');
+ if ($opt_v) { $verbose = 1; }
+
+
+@@ -609,7 +608,7 @@ sub check_valgrind_status
+ #
+ sub tempname {
+ my ($dir, $name, $suffix);
+- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+
+ foreach $suffix ("aa".."zz") {
+ $name = "$dir"."esltmp".$suffix.$$;
+diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
+old mode 100755
+new mode 100644
+index 9c77791..024ed34
+--- a/easel/testsuite/coverage_report.pl
++++ b/easel/testsuite/coverage_report.pl
+@@ -16,9 +16,9 @@
+ #
+ # SRE, Thu Mar 1 19:22:57 2007 (Janelia)
+ # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require "getopts.pl";
++use Getopt::Std;
+ $have_sloccount = 1;
+-&Getopts('cs');
++getopts('cs');
+ if ($opt_c) { $do_recompile = 1; }
+ if ($opt_s) { $have_sloccount = 0; }
+
+diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
+index 757854d..a9a8902 100755
+--- a/easel/testsuite/driver_report.pl
++++ b/easel/testsuite/driver_report.pl
+@@ -25,8 +25,8 @@
+ # SRE, Fri Mar 2 10:01:44 2007 (Janelia)
+ # SVN $Id: driver_report.pl 326 2009-02-28 15:49:07Z eddys $
+
+-require "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+
+ if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
+diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
+old mode 100755
+new mode 100644
+index 186a392..07026a0
+--- a/easel/testsuite/valgrind_report.pl
++++ b/easel/testsuite/valgrind_report.pl
+@@ -10,8 +10,8 @@
+ #
+ # SRE, Fri Mar 2 08:37:48 2007 [Janelia]
+ # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+
+ if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
+diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl
+index d4c0f67..4e8175a 100755
+--- a/profmark/rocplot.pl
++++ b/profmark/rocplot.pl
+@@ -2,8 +2,8 @@
+
+ $nsearches = 1567;
+
+-require "getopts.pl";
+-&Getopts('n:X:x:');
++use Getopt::Std
++getopts('n:X:x:');
+
+ if ($opt_n) { $nsearches = $opt_n; }
+ if ($opt_X) {
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
new file mode 100644
index 000000000000..7b1fbba5e075
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+LICENSE="GPL-2"
+HOMEPAGE="http://hmmer.janelia.org/"
+SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+IUSE="pvm threads"
+KEYWORDS="~alpha amd64 ia64 ~ppc ~sparc x86"
+
+DEPEND="pvm? ( sys-cluster/pvm )"
+
+src_compile() {
+ ./configure \
+ --host=${CHOST} \
+ --prefix="${D}"/usr \
+ --exec_prefix="${D}"/usr \
+ --mandir="${D}"/usr/share/man \
+ --enable-lfs \
+ $(use_enable pvm) \
+ $(use_enable threads) || die
+ emake || die
+}
+
+src_install() {
+ einstall || die
+
+ cd src
+ dolib libhmmer.a
+ insinto /usr/include/hmmer
+ doins *.h
+
+ cd ../squid
+ dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
+ dolib libsquid.a
+ insinto /usr/include/hmmer
+ doins *.h
+
+ cd ..
+ dodoc NOTES
+ newdoc 00README README
+ insinto /usr/share/doc/${PF}
+ doins Userguide.pdf
+}
+
+src_test() {
+ make check
+}
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
new file mode 100644
index 000000000000..64fa50030079
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+LICENSE="GPL-2"
+HOMEPAGE="http://hmmer.janelia.org/"
+SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+IUSE="pvm threads"
+KEYWORDS="~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86"
+
+DEPEND="pvm? ( sys-cluster/pvm )"
+
+src_compile() {
+ econf \
+ --host=${CHOST} \
+ --prefix="${D}"/usr \
+ --exec_prefix="${D}"/usr \
+ --mandir="${D}"/usr/share/man \
+ --enable-lfs \
+ $(use_enable pvm) \
+ $(use_enable threads) || die
+ emake || die
+}
+
+src_install() {
+ einstall || die
+
+ cd src
+ dolib libhmmer.a
+ insinto /usr/include/hmmer
+ doins *.h
+
+ cd ../squid
+ dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
+ dolib libsquid.a
+ insinto /usr/include/hmmer
+ doins *.h
+
+ cd ..
+ dodoc NOTES
+ newdoc 00README README
+ insinto /usr/share/doc/${PF}
+ doins Userguide.pdf
+}
+
+src_test() {
+ make check
+}
diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild
new file mode 100644
index 000000000000..86183e7f9d3a
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+HOMEPAGE="http://hmmer.janelia.org/"
+SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+DEPEND="
+ mpi? ( virtual/mpi )
+ gsl? ( >=sci-libs/gsl-1.12 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-fix_tests.patch \
+ "${FILESDIR}"/${P}-perl-5.16-2.patch
+}
+
+src_configure() {
+ econf \
+ $(use_enable cpu_flags_x86_sse sse) \
+ $(use_enable mpi) \
+ $(use_enable threads) \
+ $(use_with gsl)
+}
+
+src_install() {
+ default
+
+ use static-libs && dolib.a src/libhmmer.a easel/libeasel.a
+
+ insinto /usr/share/${PN}
+ doins -r tutorial
+ dodoc Userguide.pdf
+}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
new file mode 100644
index 000000000000..66fa76626615
--- /dev/null
+++ b/sci-biology/hmmer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="pvm">Add support for parallel virtual machine
+ (<pkg>sys-cluster/pvm</pkg>)</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/iedera/Manifest b/sci-biology/iedera/Manifest
new file mode 100644
index 000000000000..325eeedf3e8e
--- /dev/null
+++ b/sci-biology/iedera/Manifest
@@ -0,0 +1 @@
+DIST iedera-1.04.tar.gz 123847 SHA256 39d60b052f40476aebead981020f53e6b801293c3f13c4aea3f65a230027f39b
diff --git a/sci-biology/iedera/iedera-1.04.ebuild b/sci-biology/iedera/iedera-1.04.ebuild
new file mode 100644
index 000000000000..ad1edbcdc4d6
--- /dev/null
+++ b/sci-biology/iedera/iedera-1.04.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="A subset seed design tool for DNA sequence alignment"
+HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php"
+SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS README NEWS
+}
diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/iedera/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest
new file mode 100644
index 000000000000..ab636b70040d
--- /dev/null
+++ b/sci-biology/infernal/Manifest
@@ -0,0 +1 @@
+DIST infernal-1.0.2.tar.gz 15205421 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af WHIRLPOOL c4fa3326eb1b36252ce41ca1aeca68bed4373061ca6bc2bfc0af62c0805bfa1747272fbf223b8d47194853ae5cbe7af11d47493c258264503ea6aa7b142a6b60
diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
new file mode 100644
index 000000000000..5bc5bd008ff6
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
@@ -0,0 +1,15 @@
+Respect LDFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=338177
+
+--- src/Makefile.in
++++ src/Makefile.in
+@@ -86,7 +86,7 @@
+ all: $(PROGS)
+
+ $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS}
+- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
+
+
+ #################################################################
diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
new file mode 100644
index 000000000000..b9791fa1ca2e
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
@@ -0,0 +1,15 @@
+Fix buffer overflow
+
+http://bugs.gentoo.org/show_bug.cgi?id=338179
+
+--- easel/esl_getopts.c
++++ easel/esl_getopts.c
+@@ -1270,7 +1270,7 @@
+ "Arg looks like option? Use %.24s%.24s if you really mean it.",
+ g->opt[opti].name, *ret_optarg);
+ } else
+- ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);
++ ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);
+
+ g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */
+ }
diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
new file mode 100644
index 000000000000..004742546f00
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
@@ -0,0 +1,31 @@
+Fix parallel build
+
+http://bugs.gentoo.org/show_bug.cgi?id=311919
+
+--- Makefile.in
++++ Makefile.in
+@@ -82,9 +82,10 @@
+ all: core
+
+ core:
+- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make)
+- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module)
+- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
++ $(MAKE) -C easel
++ $(MAKE) -C src
++ $(MAKE) -C src module
++ $(MAKE) -C testsuite
+
+ #.PHONY: $(RIGFILTERS)
+ #$(RIGFILTERS): core
+--- easel/Makefile.in
++++ easel/Makefile.in
+@@ -132,7 +132,7 @@
+ esl_wuss.o
+
+ all: libeasel.a
+- (cd miniapps; make)
++ $(MAKE) -C miniapps
+
+ .c.o:
+ ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $<
diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
new file mode 100644
index 000000000000..c96dcae7b296
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
@@ -0,0 +1,147 @@
+ benchmarks/cmsearch-rmark/sre.pl | 4 +---
+ easel/devkit/autodoc | 4 ++--
+ easel/devkit/esl-dependencies | 4 ++--
+ easel/devkit/sqc | 7 +++----
+ easel/testsuite/coverage_report.pl | 4 ++--
+ easel/testsuite/driver_report.pl | 4 ++--
+ easel/testsuite/valgrind_report.pl | 4 ++--
+ 7 files changed, 14 insertions(+), 17 deletions(-)
+
+diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl
+index 9136717..e4df233 100644
+--- a/benchmarks/cmsearch-rmark/sre.pl
++++ b/benchmarks/cmsearch-rmark/sre.pl
+@@ -6,8 +6,6 @@
+
+ package SRE_perlstuff;
+
+-require "importenv.pl";
+-
+ # Function: tempname
+ #
+ # Returns a unique temporary filename.
+@@ -26,7 +24,7 @@ require "importenv.pl";
+ #
+ sub main'tempname {
+ local ($dir, $name);
+- if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
+
+ foreach $suffix ("aa".."zz") {
+ $name = "$dir/sre$suffix$$";
+diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
+old mode 100755
+new mode 100644
+index 045ce36..22268f6
+--- a/easel/devkit/autodoc
++++ b/easel/devkit/autodoc
+@@ -49,8 +49,8 @@
+ #
+ # SRE, Tue Nov 30 19:43:47 2004
+
+-require "getopts.pl";
+-&Getopts('n:t');
++use Getopt::Std;
++getopts('n:t');
+ $cfile = shift;
+
+ if ($opt_t) { $show_api_table = 1; }
+diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
+old mode 100755
+new mode 100644
+index a4dc126..b61fa7a
+--- a/easel/devkit/esl-dependencies
++++ b/easel/devkit/esl-dependencies
+@@ -13,8 +13,8 @@
+ # SRE, Mon Jun 11 11:15:31 2007
+ # SVN $Id$
+
+-require "getopts.pl"
+-&Getopts('1afr');
++use Getopt::Std;
++getopts('1afr');
+
+ if ($opt_1) { $show_summary_table = 1; }
+ if ($opt_a) { $list_augfiles = 1; }
+diff --git a/easel/devkit/sqc b/easel/devkit/sqc
+old mode 100755
+new mode 100644
+index 81d03de..6201d3d
+--- a/easel/devkit/sqc
++++ b/easel/devkit/sqc
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug 6 11:16:39 2002
+ # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
+
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+
+ # Parse our command line
+ #
+-&Getopts('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1; }
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs, $opt_r; }
+@@ -510,7 +509,7 @@ check_ccmalloc_status
+ #
+ sub tempname {
+ my ($dir, $name, $suffix);
+- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+
+ foreach $suffix ("aa".."zz") {
+ $name = "$dir"."esltmp".$suffix.$$;
+diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
+old mode 100755
+new mode 100644
+index 9c77791..024ed34
+--- a/easel/testsuite/coverage_report.pl
++++ b/easel/testsuite/coverage_report.pl
+@@ -16,9 +16,9 @@
+ #
+ # SRE, Thu Mar 1 19:22:57 2007 (Janelia)
+ # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require "getopts.pl";
++use Getopt::Std;
+ $have_sloccount = 1;
+-&Getopts('cs');
++getopts('cs');
+ if ($opt_c) { $do_recompile = 1; }
+ if ($opt_s) { $have_sloccount = 0; }
+
+diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
+old mode 100755
+new mode 100644
+index d1b4a9a..db4378f
+--- a/easel/testsuite/driver_report.pl
++++ b/easel/testsuite/driver_report.pl
+@@ -19,8 +19,8 @@
+ # SRE, Fri Mar 2 10:01:44 2007 (Janelia)
+ # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $
+
+-require "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+
+ if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
+diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
+old mode 100755
+new mode 100644
+index 186a392..07026a0
+--- a/easel/testsuite/valgrind_report.pl
++++ b/easel/testsuite/valgrind_report.pl
+@@ -10,8 +10,8 @@
+ #
+ # SRE, Fri Mar 2 08:37:48 2007 [Janelia]
+ # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+
+ if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; }
diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
new file mode 100644
index 000000000000..3c0ca9aa7b12
--- /dev/null
+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="Inference of RNA alignments"
+HOMEPAGE="http://infernal.janelia.org/"
+SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="mpi"
+KEYWORDS="amd64 x86"
+
+DEPEND="mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-parallel-build.patch \
+ "${FILESDIR}"/${P}-overflows.patch \
+ "${FILESDIR}"/${P}-perl-5.16-2.patch \
+ "${FILESDIR}"/${P}-ldflags.patch
+}
+
+src_configure() {
+ econf \
+ --prefix="${D}/usr" \
+ $(use_enable mpi)
+}
+
+src_install() {
+ default
+
+ pushd documentation/manpages > /dev/null
+ for i in *;
+ do newman ${i} ${i/.man/.1}
+ done
+ popd > /dev/null
+
+ insinto /usr/share/${PN}
+ doins -r benchmarks tutorial intro matrices
+ dodoc 00README* Userguide.pdf documentation/release-notes/*
+}
diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/infernal/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest
new file mode 100644
index 000000000000..ec521a7104b3
--- /dev/null
+++ b/sci-biology/iqpnni/Manifest
@@ -0,0 +1,3 @@
+DIST iqpnni-3.2.tar.gz 638743 SHA256 0e97a03841e3460b9e0ddadbfa27393bf370ff82725a620c8d46a1ce85e4a20f
+DIST iqpnni-3.3.1.tar.gz 650395 SHA256 bdc5873c5dd59b07b8f8c9547e86120b53fa3cd802ec7acdad61bacc4c3ac7d9
+DIST iqpnni-3.3.2.tar.gz 646603 SHA256 e4ffc783c7444bfadd40c9d55e9fb0275fcf7dca80aa3217768c9bf63c28567f
diff --git a/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch
new file mode 100644
index 000000000000..c4f49284abc1
--- /dev/null
+++ b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch
@@ -0,0 +1,13 @@
+diff -rc iqpnni-3.3.1-orig/src/constant.h iqpnni-3.3.1/src/constant.h
+*** iqpnni-3.3.1-orig/src/constant.h 2009-01-04 19:33:35.000000000 -0500
+--- iqpnni-3.3.1/src/constant.h 2009-01-04 19:40:21.000000000 -0500
+***************
+*** 36,41 ****
+--- 36,42 ----
+ #include <stdio.h>
+ #include <math.h>
+ #include <string>
++ #include <string.h>
+
+ using namespace std;
+
diff --git a/sci-biology/iqpnni/iqpnni-3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.2.ebuild
new file mode 100644
index 000000000000..070e962fb311
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install() {
+ dobin src/iqpnni
+
+ dodoc ChangeLog AUTHORS README NEWS TODO
+ if use doc ; then
+ dohtml manual/iqpnni-manual.html
+ insinto /usr/share/doc/${P}
+ doins manual/iqpnni-manual.pdf
+ fi
+}
diff --git a/sci-biology/iqpnni/iqpnni-3.3.1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild
new file mode 100644
index 000000000000..8916e7e51608
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_install() {
+ dobin src/iqpnni
+
+ dodoc ChangeLog AUTHORS README NEWS TODO
+ if use doc ; then
+ dohtml manual/iqpnni-manual.html
+ insinto /usr/share/doc/${P}
+ doins manual/iqpnni-manual.pdf
+ fi
+}
diff --git a/sci-biology/iqpnni/iqpnni-3.3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild
new file mode 100644
index 000000000000..e9939ef0f506
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install() {
+ dobin src/iqpnni
+
+ dodoc ChangeLog AUTHORS README NEWS TODO
+ if use doc ; then
+ dohtml manual/iqpnni-manual.html
+ insinto /usr/share/doc/${P}
+ doins manual/iqpnni-manual.pdf
+ fi
+}
diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/iqpnni/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest
new file mode 100644
index 000000000000..6250f54bc17b
--- /dev/null
+++ b/sci-biology/kalign/Manifest
@@ -0,0 +1 @@
+DIST kalign_2.03.orig.tar.gz 114022 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0
diff --git a/sci-biology/kalign/kalign-2.03-r1.ebuild b/sci-biology/kalign/kalign-2.03-r1.ebuild
new file mode 100644
index 000000000000..4422bad730c0
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03-r1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+ sed \
+ -e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \
+ -i Makefile.in || die
+}
+
+src_compile() {
+ emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}"
+}
+
+src_install() {
+ dobin ${PN}
+ dodoc README
+}
diff --git a/sci-biology/kalign/kalign-2.03.ebuild b/sci-biology/kalign/kalign-2.03.ebuild
new file mode 100644
index 000000000000..3862e49eaf7f
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+ unpack ${A}
+ sed -i 's/^CFLAGS.*= -O9/CFLAGS := ${CFLAGS} -O3/' "${S}"/Makefile.in
+}
+
+src_install() {
+ dobin kalign
+ dodoc README
+}
diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/kalign/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
new file mode 100644
index 000000000000..fb04603869dd
--- /dev/null
+++ b/sci-biology/lagan/Manifest
@@ -0,0 +1 @@
+DIST lagan20.tar.gz 589115 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch
new file mode 100644
index 000000000000..e324ef64c4c6
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-flags.patch
@@ -0,0 +1,107 @@
+diff --git a/Makefile b/Makefile
+index fbbbe79..a1d449b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+ all:
+- (cd src; $(MAKE))
++ $(MAKE) -C src
+ clean:
+ rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
+ (cd src; $(MAKE) clean)
+diff --git a/src/Makefile b/src/Makefile
+index 7f6b6fd..dd6309b 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
+ TRGT_DIR = ..
+
+ all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
+- (cd glocal; $(MAKE))
++ $(MAKE) -C glocal
+ clean:
+ rm -f *.o *~ utils/*~ mlagan.purify core
+ (cd glocal; $(MAKE) clean)
+ ../anchors: anchors.c skiplist.c
+- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ ../order: order.c diagmatrix.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../utils/bin2mf: utils/bin2mf.c
+- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ ../utils/bin2bl: utils/bin2bl.c
+- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ ../utils/cextract: utils/cextract.c
+- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ ../utils/cstat: utils/cstat.c
+- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ ../utils/contigorder: utils/contigorder.c
+- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ ../utils/getbounds: utils/getbounds.c
+- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ ../utils/getcontigpos: utils/getcontigpos.c
+- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ ../utils/getlength: utils/getlength.c
+- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ ../utils/getoverlap: utils/getoverlap.c
+- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ ../utils/rc: utils/rc.c
+- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ ../utils/seqmerge: utils/seqmerge.c
+- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ ../utils/scorealign: utils/scorealign.c
+- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ ../utils/scorecontigs: utils/scorecontigs.c
+- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ ../utils/fa2xfa: utils/fa2xfa.c
+- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ ../utils/overlay: utils/overlay.c
+- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ ../utils/Glue: utils/Glue.cpp
+- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ ../utils/dotplot: utils/dotplot.cpp
+- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+diff --git a/src/glocal/Makefile b/src/glocal/Makefile
+index ce1421a..b82507f 100755
+--- a/src/glocal/Makefile
++++ b/src/glocal/Makefile
+@@ -10,10 +10,10 @@ TRGT = glocal
+ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
+
+ .cpp.o:
+- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
++ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
+
+ $(TRGT): $(OBJECTS)
+- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
++ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+
+ clean :
+ rm -f *.o ./*~ *~ core
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
new file mode 100644
index 000000000000..a4b1d6808e2f
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
@@ -0,0 +1,23 @@
+diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
+--- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000
++++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+
+diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
+--- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000
++++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000
+@@ -1,6 +1,7 @@
+ #include "MultiSequence.h"
+ #include "SafeVector.h"
+ #include "Output.h"
++#include <string.h>
+ #include <math.h>
+ #include <assert.h>
+ #include <fstream>
diff --git a/sci-biology/lagan/lagan-2.0-r1.ebuild b/sci-biology/lagan/lagan-2.0-r1.ebuild
new file mode 100644
index 000000000000..63b966e79ef0
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils
+
+MY_P="lagan20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die
+ # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
+ sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
+ epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_install() {
+ dobin lagan.pl slagan.pl mlagan
+ rm lagan.pl slagan.pl utils/Utils.pm
+ dodir /usr/share/${PN}/lib
+ insinto /usr/share/${PN}/lib
+ doins Utils.pm
+ exeinto /usr/share/${PN}/utils
+ doexe utils/*
+ exeinto /usr/share/${PN}
+ doexe *.pl anchors chaos glocal order prolagan
+ insinto /usr/share/${PN}
+ doins *.txt
+ dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap
+ dosym /usr/bin/lagan.pl /usr/bin/lagan
+ dosym /usr/bin/slagan.pl /usr/bin/slagan
+ echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN}
+ doenvd "${S}/99${PN}"
+ dodoc Readmes/README.*
+}
diff --git a/sci-biology/lagan/lagan-2.0-r2.ebuild b/sci-biology/lagan/lagan-2.0-r2.ebuild
new file mode 100644
index 000000000000..a37a3736de08
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
+ # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
+ sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
+ epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_compile() {
+ emake \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ CXXFLAGS="${CXXFLAGS}" \
+ CFLAGS="${CFLAGS}"
+}
+
+src_install() {
+ newbin lagan.pl lagan || die
+ newbin slagan.pl slagan || die
+ dobin mlagan || die
+ rm lagan.pl slagan.pl utils/Utils.pm
+
+ insinto /usr/$(get_libdir)/${PN}/lib
+ doins Utils.pm || die
+ exeinto /usr/$(get_libdir)/${PN}/utils
+ doexe utils/* || die
+ exeinto /usr/$(get_libdir)/${PN}
+ doexe *.pl anchors chaos glocal order prolagan || die
+ insinto /usr/$(get_libdir)/${PN}
+ doins *.txt || die
+ dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
+ echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > ${S}/99${PN}
+ doenvd "${S}/99${PN}" || die
+ dodoc Readmes/README.* || die
+}
diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/lagan/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
new file mode 100644
index 000000000000..0fad882975fa
--- /dev/null
+++ b/sci-biology/last/Manifest
@@ -0,0 +1,2 @@
+DIST last-230.zip 418077 SHA256 8d55ee95e05a08afa72690df9086886e97142adcfbf750cf5cf6015b91215484 SHA512 46c858c2bd4a9aa00ac3b448ce78bdee6c1edd4f6569cff3c81ec8a7c661d89a9b5e7a888cbc6da190b243f0ec83c485b4574dadc6a58669d9b955eb70c329d1 WHIRLPOOL aaa0483a58821cca0fdd7875cb4e7c62493fd724729d957df1d51c7612e92e3acefae2727789f63a248f02c976a45c3209d6bac2c39f54d84f02d1106c2d0f85
+DIST last-299.zip 453159 SHA256 cc68e9c0b5220da67fd0239c9663dc0d1a05e63b337a6c98cfef6d5c38d0c54c SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b WHIRLPOOL 12e826c22c2d91845e89aa0c6e99af785973e8a276dec4f97ed292e144327c7c58024622d3f7285c6107bca7af1bf3c29a23ec9d22dc88ff5dc041a0df96f3ce
diff --git a/sci-biology/last/files/162-gcc46.patch b/sci-biology/last/files/162-gcc46.patch
new file mode 100644
index 000000000000..9c66c6d39f00
--- /dev/null
+++ b/sci-biology/last/files/162-gcc46.patch
@@ -0,0 +1,15 @@
+ src/XdropAligner.hh | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/XdropAligner.hh b/src/XdropAligner.hh
+index 9dea32e..3c0e35f 100644
+--- a/src/XdropAligner.hh
++++ b/src/XdropAligner.hh
+@@ -12,6 +12,7 @@
+ #include <vector>
+ #include <cassert>
+ #include <climits> // INT_MAX
++#include <cstddef>
+
+ namespace cbrc{
+
diff --git a/sci-biology/last/files/162-ldflags.patch b/sci-biology/last/files/162-ldflags.patch
new file mode 100644
index 000000000000..e5dd3ee2234e
--- /dev/null
+++ b/sci-biology/last/files/162-ldflags.patch
@@ -0,0 +1,16 @@
+ src/makefile | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/makefile b/src/makefile
+index e77ffa7..92e4575 100644
+--- a/src/makefile
++++ b/src/makefile
+@@ -51,7 +51,7 @@ lastal: $(ALSRC) $(ALINC) makefile $(OBJ)
+ $(CXX) $(STRICT) $(CXXFLAGS) -o $@ $(ALSRC) $(OBJ)
+
+ lastex: $(EXSRC) $(EXINC) makefile
+- $(CXX) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC)
++ $(CXX) $(STRICT) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC)
+
+ $(OBJ): CA_code/*.c CA_code/*.h makefile
+ $(CC) $(CFLAGS) -c CA_code/lambda_calculator.c
diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild
new file mode 100644
index 000000000000..51dc9ee0faf0
--- /dev/null
+++ b/sci-biology/last/last-230.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/archive/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+ sed \
+ -e 's:-o $@:$(LDFLAGS) -o $@:g' \
+ -i src/makefile || die
+}
+
+src_compile() {
+ emake \
+ -e -C src \
+ CXX="$(tc-getCXX)" \
+ CC="$(tc-getCC)" \
+ STRICT="" || die
+}
+
+src_install() {
+ dobin src/last{al,db,ex}
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+ dodoc doc/*.txt ChangeLog.txt README.txt
+}
diff --git a/sci-biology/last/last-299.ebuild b/sci-biology/last/last-299.ebuild
new file mode 100644
index 000000000000..9d32fdf11c3c
--- /dev/null
+++ b/sci-biology/last/last-299.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils toolchain-funcs python-r1
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+ sed \
+ -e 's:-o $@:$(LDFLAGS) -o $@:g' \
+ -i src/makefile || die
+}
+
+src_compile() {
+ emake \
+ -e -C src \
+ CXX="$(tc-getCXX)" \
+ CC="$(tc-getCC)" \
+ STRICT="" || die
+}
+
+src_install() {
+ local i
+
+ dobin src/last{al,db,ex}
+
+ dodoc doc/*.txt ChangeLog.txt README.txt
+ dohtml doc/*html
+
+ cd scripts || die
+ for i in *py; do
+ python_parallel_foreach_impl python_newscript ${i} ${i%.py}
+ done
+ dobin *sh
+}
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/last/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
new file mode 100644
index 000000000000..0f4b923df331
--- /dev/null
+++ b/sci-biology/mafft/Manifest
@@ -0,0 +1,2 @@
+DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49
+DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4
diff --git a/sci-biology/mafft/files/6.811-respect.patch b/sci-biology/mafft/files/6.811-respect.patch
new file mode 100644
index 000000000000..ebfb2c7be7b8
--- /dev/null
+++ b/sci-biology/mafft/files/6.811-respect.patch
@@ -0,0 +1,192 @@
+diff --git a/core/Makefile b/core/Makefile
+index 8bb8baf..cf28559 100644
+--- a/core/Makefile
++++ b/core/Makefile
+@@ -1,5 +1,5 @@
+ PREFIX = /usr/local
+-LIBDIR = $(PREFIX)/lib/mafft
++LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
+ BINDIR = $(PREFIX)/bin
+ MANDIR = $(PREFIX)/man/man1
+
+@@ -127,136 +127,136 @@ mltaln.h : functions.h
+ touch mltaln.h
+
+ ord : $(OBJORD)
+- $(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
+
+ tbfast : $(OBJTBFAST)
+- $(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
+
+ tbfast2 : $(OBJTBFAST2)
+- $(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
+
+ disttbfast : $(OBJDISTTBFAST)
+- $(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
+
+ splittbfast : $(OBJSPLITTBFAST)
+- $(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
+
+ splitfromaln : $(OBJSPLITFROMALN)
+- $(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
+
+ splittbfast2 : $(OBJSPLITTBFAST2)
+- $(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
+
+ dummy : $(OBJDUMMY)
+- $(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
+
+ setcore : $(OBJSETCORE)
+- $(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
+
+ countlen : $(OBJCOUNTLEN)
+- $(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
+
+ seq2regtable : $(OBJSEQ2REGTABLE)
+- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
+
+ regtable2seq : $(OBJREGTABLE2SEQ)
+- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
+
+ f2cl : $(OBJF2CL)
+- $(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
+
+ mccaskillwrap : $(OBJMCCASKILLWRAP)
+- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
+
+ contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
+
+ pairlocalalign : $(OBJPAIRLOCALALIGN)
+- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
+
+ pairash : $(OBJPAIRASH)
+- $(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
+
+ rnatest : $(OBJRNATEST)
+- $(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
+
+ pair2hat3s : $(OBJPAIR2HAT3S)
+- $(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
+
+ multi2hat3s : $(OBJMULTI2HAT3S)
+- $(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
+
+ getlag : $(OBJGETLAG)
+- $(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
+
+ tditr : $(OBJTDITR)
+- $(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
+
+ dvtditr : $(OBJDVTDITR)
+- $(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
+
+ mafft-profile : $(OBJGALN)
+- $(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
+
+ gapfill : $(OBJGAPFILL)
+- $(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
+
+ dndfast4 : $(OBJDNDFAST4)
+- $(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
+
+ dndfast5 : $(OBJDNDFAST5)
+- $(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
+
+ dndfast6 : $(OBJDNDFAST6)
+- $(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
+
+ dndfast7 : $(OBJDNDFAST7)
+- $(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
+
+ dndblast : $(OBJDNDBLAST)
+- $(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
+
+ dndfast3 : $(OBJDNDFAST3)
+- $(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
+
+ triplet : $(OBJTRIPLET)
+- $(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
+
+ triplet3 : $(OBJTRIPLET3)
+- $(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
+
+ sextet3 : $(OBJSEXTET3)
+- $(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
+
+ sextet4 : $(OBJSEXTET4)
+- $(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
+
+ sextet5 : $(OBJSEXTET5)
+- $(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
+
+ mafft-distance : $(OBJDISTANCE)
+- $(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
+
+ triplet5 : $(OBJTRIPLET5)
+- $(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
+
+ triplet6 : $(OBJTRIPLET6)
+- $(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
+
+ octet4 : $(OBJOCTET4)
+- $(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
+
+ dndpre : $(OBJDNDPRE)
+- $(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
+
+ dndpre2 : $(OBJDNDPRESCORE)
+- $(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
+
+ score : $(OBJSCORE)
+- $(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
+
+ genMtx : $(OBJGENMTX)
+- $(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
+
+ gapfill.o : gapfill.c $(HEADER)
+ $(CC) $(CFLAGS) -c gapfill.c
diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch
new file mode 100644
index 000000000000..6fba7153622d
--- /dev/null
+++ b/sci-biology/mafft/files/mafft-7.037-respect.patch
@@ -0,0 +1,217 @@
+ core/Makefile | 100 +++++++++++++++++++++++++++++-----------------------------
+ 1 file changed, 50 insertions(+), 50 deletions(-)
+
+diff --git a/core/Makefile b/core/Makefile
+index 9acebb3..3838a45 100644
+--- a/core/Makefile
++++ b/core/Makefile
+@@ -145,151 +145,151 @@ mltaln.h : functions.h
+ touch mltaln.h
+
+ version : version.c mltaln.h
+- $(CC) -o $@ version.c $(MYCFLAGS)
++ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS)
+
+ tbfast : $(OBJTBFAST)
+- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
+
+ addsingle : $(OBJADDSINGLE)
+- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS)
+
+ tbfast2 : $(OBJTBFAST2)
+- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
+
+ disttbfast : $(OBJDISTTBFAST)
+- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
+
+ makedirectionlist : $(OBJMAKEDIRECTIONLIST)
+- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS)
+
+ splittbfast : $(OBJSPLITTBFAST)
+- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
+
+ splitfromaln : $(OBJSPLITFROMALN)
+- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
+
+ splittbfast2 : $(OBJSPLITTBFAST2)
+- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
+
+ dummy : $(OBJDUMMY)
+- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
+
+ setcore : $(OBJSETCORE)
+- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
+
+ countlen : $(OBJCOUNTLEN)
+- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
+
+ seq2regtable : $(OBJSEQ2REGTABLE)
+- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
+
+ regtable2seq : $(OBJREGTABLE2SEQ)
+- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
+
+ setdirection : $(OBJSETDIRECTION)
+- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS)
+
+ replaceu : $(OBJREPLACEU)
+- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
+
+ restoreu : $(OBJRESTOREU)
+- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
+
+ f2cl : $(OBJF2CL)
+- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
+
+ mccaskillwrap : $(OBJMCCASKILLWRAP)
+- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
+
+ contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
+
+ pairlocalalign : $(OBJPAIRLOCALALIGN)
+- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
+
+ pairash : $(OBJPAIRASH)
+- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
+
+ rnatest : $(OBJRNATEST)
+- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
+
+ pair2hat3s : $(OBJPAIR2HAT3S)
+- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
+
+ multi2hat3s : $(OBJMULTI2HAT3S)
+- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
+
+ getlag : $(OBJGETLAG)
+- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
+
+ tditr : $(OBJTDITR)
+- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
+
+ dvtditr : $(OBJDVTDITR)
+- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
+
+ mafft-profile : $(OBJGALN)
+- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
+
+ gapfill : $(OBJGAPFILL)
+- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
+
+ dndfast4 : $(OBJDNDFAST4)
+- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
+
+ dndfast5 : $(OBJDNDFAST5)
+- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
+
+ dndfast6 : $(OBJDNDFAST6)
+- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
+
+ dndfast7 : $(OBJDNDFAST7)
+- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
+
+ dndblast : $(OBJDNDBLAST)
+- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
+
+ dndfast3 : $(OBJDNDFAST3)
+- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
+
+ triplet : $(OBJTRIPLET)
+- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
+
+ triplet3 : $(OBJTRIPLET3)
+- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
+
+ sextet3 : $(OBJSEXTET3)
+- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
+
+ sextet4 : $(OBJSEXTET4)
+- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
+
+ sextet5 : $(OBJSEXTET5)
+- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
+
+ mafft-distance : $(OBJDISTANCE)
+- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
+
+ triplet5 : $(OBJTRIPLET5)
+- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
+
+ triplet6 : $(OBJTRIPLET6)
+- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
+
+ octet4 : $(OBJOCTET4)
+- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
+
+ dndpre : $(OBJDNDPRE)
+- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
+
+ dndpre2 : $(OBJDNDPRESCORE)
+- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
+
+ score : $(OBJSCORE)
+- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
+
+ genMtx : $(OBJGENMTX)
+- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
+
+ gapfill.o : gapfill.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c gapfill.c
+@@ -525,7 +525,7 @@ install : all
+ chmod 755 $(SCRIPTS)
+ $(INSTALL) $(SCRIPTS) $(BINDIR)
+ chmod 755 $(PROGS)
+- $(INSTALL) -s $(PROGS) $(LIBDIR)
++ $(INSTALL) $(PROGS) $(LIBDIR)
+ $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR)
+
+ ( cd $(BINDIR); \
diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
new file mode 100644
index 000000000000..d064e73b8089
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.050.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+EXTENSIONS="-without-extensions"
+
+DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-7.037-respect.patch
+ use threads && append-cppflags -Denablemultithread
+ sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
+ sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
+}
+
+src_compile() {
+ pushd core > /dev/null || die
+ emake \
+ $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+ PREFIX="${EPREFIX}"/usr \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS}"
+ popd > /dev/null || die
+}
+
+src_test() {
+ export MAFFT_BINARIES="${S}"/core
+ cd test || die
+ bash ../core/mafft sample > test.fftns2 || die
+ bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
+ bash ../core/mafft --globalpair sample > test.gins1 || die
+ bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
+ bash ../core/mafft --localpair sample > test.lins1 || die
+ bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
+
+ diff test.fftns2 sample.fftns2 || die
+ diff test.fftnsi sample.fftnsi || die
+ diff test.gins1 sample.gins1 || die
+ diff test.ginsi sample.ginsi || die
+ diff test.lins1 sample.lins1 || die
+}
+
+src_install() {
+ pushd core
+ emake PREFIX="${ED}usr" install
+ popd
+ dodoc readme
+}
diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild
new file mode 100644
index 000000000000..b76c0e60839a
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.215.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+EXTENSIONS="-without-extensions"
+
+DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+# epatch "${FILESDIR}"/${PN}-7.037-respect.patch
+ use threads && append-cppflags -Denablemultithread
+# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
+ sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
+ sed \
+ -e 's:$(LDFLAGS)::g' \
+ -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \
+ -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \
+ -e '/INSTALL/s: -s : :g' \
+ -i core/Makefile || die
+}
+
+src_compile() {
+ cd core || die
+ emake \
+ $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+ PREFIX="${EPREFIX}"/usr \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS} -Wno-unused-result"
+}
+
+src_test() {
+ export MAFFT_BINARIES="${S}"/core
+ cd test || die
+ bash ../core/mafft sample > test.fftns2 || die
+ bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
+ bash ../core/mafft --globalpair sample > test.gins1 || die
+ bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
+ bash ../core/mafft --localpair sample > test.lins1 || die
+ bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
+
+ diff test.fftns2 sample.fftns2 || die
+ diff test.fftnsi sample.fftnsi || die
+ diff test.gins1 sample.gins1 || die
+ diff test.ginsi sample.ginsi || die
+ diff test.lins1 sample.lins1 || die
+}
+
+src_install() {
+ dodoc readme
+ cd core || die
+ emake PREFIX="${ED}usr" install
+}
diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mafft/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mammoth/Manifest b/sci-biology/mammoth/Manifest
new file mode 100644
index 000000000000..584405eb5350
--- /dev/null
+++ b/sci-biology/mammoth/Manifest
@@ -0,0 +1 @@
+DIST mammoth-1.0-src.tgz 319617 SHA256 7a21bc47db4a47cc5ebeeb4c46761a79eece0a802104a3d6189f388a03e59de2
diff --git a/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
new file mode 100644
index 000000000000..63bf9f246750
--- /dev/null
+++ b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
@@ -0,0 +1,21 @@
+http://gcc.gnu.org/onlinedocs/gcc-4.2.2/gfortran/SYSTEM.html#SYSTEM
+
+This intrinsic is provided in both subroutine and function forms;
+however, only one form can be used in any given program unit.
+
+--- src/6apply_rot_tras.f.orig 2007-12-10 00:51:35.000000000 -0800
++++ src/6apply_rot_tras.f 2007-12-10 00:55:07.000000000 -0800
+@@ -47,11 +47,11 @@
+ endif
+
+
+- call system ('echo $PWD > junk1')
++ i = system ('echo $PWD > junk1')
+ open(unit=21,file='junk1')
+ read(21,'(a340)', end=7) path
+ 7 close(21)
+- call system ('rm -f junk1')
++ i = system ('rm -f junk1')
+
+ c write(6,*)'my path is ', path
+ c write(6,*)tras1,tras2,tras3,
diff --git a/sci-biology/mammoth/mammoth-1.0-r1.ebuild b/sci-biology/mammoth/mammoth-1.0-r1.ebuild
new file mode 100644
index 000000000000..750d95dd894b
--- /dev/null
+++ b/sci-biology/mammoth/mammoth-1.0-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils fortran-2 flag-o-matic toolchain-funcs
+
+MY_P="${P}-src"
+
+DESCRIPTION="MAtching Molecular Models Obtained from THeory"
+HOMEPAGE="http://ub.cbm.uam.es/software.php"
+SRC_URI="${MY_P}.tgz"
+
+LICENSE="mammoth"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+S=${WORKDIR}/${MY_P}
+
+pkg_nofetch() {
+ einfo "Download the source code for MAMMOTH from"
+ einfo "${HOMEPAGE}"
+ einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+ # Broken with gfortran without this patch
+ epatch "${FILESDIR}"/${PV}-consistent-system-intrinsic.patch
+
+ case $(tc-getFC) in
+ g77) append-fflags -ffixed-line-length-none ;;
+ gfortran) append-fflags -ffixed-line-length-none ;;
+ esac
+
+ # It comes with a custom-modified configure for some reason,
+ # which forces you to pass in the Fortran compiler as a parameter.
+ # Let's do the standard stuff instead.
+ eautoreconf
+}
diff --git a/sci-biology/mammoth/metadata.xml b/sci-biology/mammoth/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mammoth/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest
new file mode 100644
index 000000000000..b5eb751fe292
--- /dev/null
+++ b/sci-biology/maq/Manifest
@@ -0,0 +1,2 @@
+DIST calib-36.dat.gz 196371 SHA256 d4480e04446eb273f1908add709dd5a24262c08a59a1647b9a2d053f4d30181b
+DIST maq-0.7.1.tar.bz2 368645 SHA256 e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2
diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
new file mode 100644
index 000000000000..9f4247d441f5
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
@@ -0,0 +1,16 @@
+ simulate.c | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/simulate.c b/simulate.c
+index 788c440..67ba2ba 100644
+--- a/simulate.c
++++ b/simulate.c
+@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres)
+ memset(wc_single, 0, 40); memset(tot_single, 0, 40);
+ memset(wc_pair, 0, 40); memset(tot_pair, 0, 40);
+ memset(abpair, 0, 4 * 256 * 10);
+- memset(tc[2], 0, 4 * sizeof(int));
++ memset(tc, 0, 4 * sizeof(int));
+ while (maqmap_read1(fp, m1)) {
+ int is_correct;
+ bit32_t p1, p2;
diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch
new file mode 100644
index 000000000000..721e53248b7a
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-flags.patch
@@ -0,0 +1,24 @@
+ configure.ac | 3 ++-
+ 1 files changed, 2 insertions(+), 1 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index ad2f1e6..4f9d7be 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -8,6 +8,7 @@ AC_PROG_CXX
+
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
++user_CXXFLAGS=${CXXFLAGS}
+ generic_CFLAGS="-Wall"
+ ext_CFLAGS=""
+ case "${host_cpu}-${host_os}" in
+@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread, [ --enable-shortreads use shortread mode],
+ AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
+ [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}"
+-CXXFLAGS=$CFLAGS
++CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}"
+
+ AC_STDC_HEADERS
+ AC_CHECK_HEADER(zlib.h)
diff --git a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch
new file mode 100644
index 000000000000..4b97da89be48
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch
@@ -0,0 +1,34 @@
+ stdhash.hh | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/stdhash.hh b/stdhash.hh
+index eaf98af..16cd1a3 100644
+--- a/stdhash.hh
++++ b/stdhash.hh
+@@ -412,7 +412,7 @@ public:
+ inline bool insert(const keytype_t &key) {
+ __lh3_hash_base_class<keytype_t>::rehash();
+ hashint_t i;
+- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ if (ret == 0) return true;
+ if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
+ else ++(this->n_size); // then ret == 2
+@@ -493,7 +493,7 @@ public:
+ inline bool insert(const keytype_t &key, const valtype_t &val) {
+ rehash();
+ hashint_t i;
+- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ vals[i] = val;
+ if (ret == 0) return true;
+ if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
+@@ -503,7 +503,7 @@ public:
+ inline bool insert(const keytype_t &key, valtype_t **q) {
+ rehash();
+ hashint_t i;
+- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ *q = vals + i;
+ if (ret == 0) return true;
+ if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
diff --git a/sci-biology/maq/maq-0.7.1-r1.ebuild b/sci-biology/maq/maq-0.7.1-r1.ebuild
new file mode 100644
index 000000000000..645a2d65a620
--- /dev/null
+++ b/sci-biology/maq/maq-0.7.1-r1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools eutils
+
+DESCRIPTION="Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="
+ mirror://sourceforge/${PN}/${P}.tar.bz2
+ mirror://sourceforge/${PN}/calib-36.dat.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-flags.patch \
+ "${FILESDIR}"/${P}-bfr-overfl.patch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ sed \
+ -e '/ext_CFLAGS/s:-m64::g' \
+ -i configure* || die
+ eautoreconf
+}
+
+src_install() {
+ default
+ insinto /usr/share/maq
+ doins "${WORKDIR}"/*.dat
+ doman maq.1
+ dodoc ${PN}.pdf
+}
diff --git a/sci-biology/maq/maq-0.7.1.ebuild b/sci-biology/maq/maq-0.7.1.ebuild
new file mode 100644
index 000000000000..1089eefbae04
--- /dev/null
+++ b/sci-biology/maq/maq-0.7.1.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2
+ mirror://sourceforge/${PN}/calib-36.dat.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND=""
+
+src_install() {
+ emake DESTDIR="${D}" install || die
+ insinto /usr/share/maq
+ doins "${WORKDIR}"/*.dat || die
+ doman maq.1
+ dodoc AUTHORS ChangeLog NEWS maq.pdf
+}
diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml
new file mode 100644
index 000000000000..79ebcc09421b
--- /dev/null
+++ b/sci-biology/maq/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">maq</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
new file mode 100644
index 000000000000..f9ad87f8424e
--- /dev/null
+++ b/sci-biology/maqview/Manifest
@@ -0,0 +1 @@
+DIST maqview-0.2.5.tar.gz 383410 SHA256 156794f114a00bb455a47ccefa50782441dc1b9668b6e7439ce0674060c085cb SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 WHIRLPOOL 0ba5a15a1317b4bb78458b9e282348983be9e2c30980aef4e35a9f5dacfff57226eaa4403fb0b9d9d448ba033409d548db224ed544ad365226a8fb59be8b743e
diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch
new file mode 100644
index 000000000000..92b9a3ed58ac
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-ldflags.patch
@@ -0,0 +1,46 @@
+ configure.ac | 18 +++---------------
+ 1 files changed, 3 insertions(+), 15 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 90e612b..5a00d15 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -9,17 +9,10 @@ AC_PROG_INSTALL
+ AC_STDC_HEADERS
+
+ is_static=0
+-case ${prefix} in
+- NONE);;
+- *) is_static=1
+- AC_MSG_WARN([Library libglut will be statically linked.])
+- LDFLAGS="-L${prefix}/lib"
+- CPPFLAGS="-I${prefix}/include";;
+-esac
+
+ # set CFLAGS and LDFLAGS
+
+-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS"
++true_CFLAGS="-DMAQ_LONGREADS"
+ case "${host_os}" in
+ darwin*)
+ GLLIBS="-framework OpenGL -framework GLUT"
+@@ -30,17 +23,12 @@ case "${host_os}" in
+ i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";;
+ esac
+ AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"])
+- AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)],
+- [is_static=1])
+- case $is_static in
+- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";;
+- 0) GLLIBS="-lGL -lglut -lm";;
+- esac
++ GLLIBS="-lGL -lglut -lm -lGLU"
+ AC_SUBST([GLLIBS]);;
+ # *) AC_MSG_ERROR([OS is not supported]);;
+ esac
+ AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1])
+-CFLAGS=$true_CFLAGS
++CFLAGS="${CFLAGS} $true_CFLAGS"
+
+ AC_CONFIG_FILES([Makefile])
+ AC_OUTPUT
diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch
new file mode 100644
index 000000000000..cd35273de66b
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-zlib.patch
@@ -0,0 +1,33 @@
+ Makefile.am | 6 +++---
+ zrio.c | 2 +-
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index dad515a..9617eb7 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,8 +1,8 @@
+ bin_PROGRAMS = zrio maqindex maqview maqindex_socks
+-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \
+- infback.c inftrees.c trees.c uncompr.c zutil.c
+-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src)
++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c
++LIBS = -lz
+ zrio_SOURCES = zrio_main.c $(generic_src)
++zrio_LDADD = -lz
+ maqindex_SOURCES = maqmap_index_main.c $(generic_src)
+ maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \
+ $(generic_src)
+diff --git a/zrio.c b/zrio.c
+index ffed00a..fe744df 100644
+--- a/zrio.c
++++ b/zrio.c
+@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void
+ totin += strm.avail_in;
+ totout += strm.avail_out;
+ tmp = strm.avail_out;
+- ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */
++ ret = inflate(&strm, Z_BLOCK); /* return at end of block */
+ totin -= strm.avail_in;
+ totout -= strm.avail_out;
+ if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout);
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
new file mode 100644
index 000000000000..043208bb79b5
--- /dev/null
+++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
@@ -0,0 +1,16 @@
+ stdhash.hh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/stdhash.hh b/stdhash.hh
+index eaf98af..f22c5a6 100644
+--- a/stdhash.hh
++++ b/stdhash.hh
+@@ -493,7 +493,7 @@ public:
+ inline bool insert(const keytype_t &key, const valtype_t &val) {
+ rehash();
+ hashint_t i;
+- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ vals[i] = val;
+ if (ret == 0) return true;
+ if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
diff --git a/sci-biology/maqview/maqview-0.2.5-r2.ebuild b/sci-biology/maqview/maqview-0.2.5-r2.ebuild
new file mode 100644
index 000000000000..e549497830bd
--- /dev/null
+++ b/sci-biology/maqview/maqview-0.2.5-r2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="mirror://sourceforge/maq/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="
+ media-libs/freeglut
+ sys-libs/zlib"
+RDEPEND="${DEPEND}
+ sci-biology/maq"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+ "${FILESDIR}"/${PV}-ldflags.patch
+ "${FILESDIR}"/${PV}-zlib.patch
+ "${FILESDIR}"/${P}-gcc4.7.patch
+ )
diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml
new file mode 100644
index 000000000000..79ebcc09421b
--- /dev/null
+++ b/sci-biology/maqview/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">maq</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mauve/mauve-9999.ebuild b/sci-biology/mauve/mauve-9999.ebuild
new file mode 100644
index 000000000000..1c3446707e4d
--- /dev/null
+++ b/sci-biology/mauve/mauve-9999.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+ESVN_REPO_URI="https://mauve.svn.sourceforge.net/svnroot/mauve/mauve/trunk"
+
+WANT_ANT_TASKS="ant-nodeps"
+EANT_GENTOO_CLASSPATH="biojava,zeus-jscl,dbus-java"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+JAVA_PKG_BSFIX_NAME="build.xml"
+
+inherit subversion java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="Multiple genome alignment with large-scale evolutionary events (GUI component)"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="doc"
+KEYWORDS=""
+
+CDEPEND="~sci-biology/biojava-1.6
+ >=dev-java/dbus-java-2.5.1
+ ~dev-java/zeus-jscl-1.08
+ dev-java/ant-nodeps"
+RDEPEND=">=virtual/jre-1.5
+ sci-biology/mauvealigner
+ ${CDEPEND}"
+DEPEND=">=virtual/jdk-1.5
+ media-gfx/icoutils
+ ${CDEPEND}"
+
+S="${WORKDIR}"
+
+java_prepare() {
+ find -name '*.jar' -not -name 'jarbundler*' -print -delete
+ perl -i -ne 'print unless /<dmg/ or /<taskdef.+name="dmg"/../<\/taskdef>/' build.xml
+ perl -i -ne 'print unless /<ssh/../<\/ssh/ or /<taskdef.+name="ssh"/../<\/taskdef>/' build.xml
+ perl -i -ne 'print unless /<retroweaver/ or /<taskdef.+name="retroweaver"/../<\/taskdef>/' build.xml
+}
+
+src_install() {
+ java-pkg_dojar Mauve.jar
+
+ java-pkg_dolauncher Mauve --main org.gel.mauve.gui.Mauve
+
+ icotool -x win32/mauve.ico
+ insinto /usr/share/pixmaps
+ newins mauve_4_48x48x32.png Mauve.png
+ make_desktop_entry Mauve Mauve Mauve
+}
diff --git a/sci-biology/mauve/metadata.xml b/sci-biology/mauve/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mauve/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mauvealigner/mauvealigner-9999.ebuild b/sci-biology/mauvealigner/mauvealigner-9999.ebuild
new file mode 100644
index 000000000000..cee185340513
--- /dev/null
+++ b/sci-biology/mauvealigner/mauvealigner-9999.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+ESVN_REPO_URI="https://mauve.svn.sourceforge.net/svnroot/mauve/mauveAligner/trunk"
+
+inherit subversion autotools
+
+DESCRIPTION="Multiple genome alignment with large-scale evolutionary events (aligner component)"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI=""
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="doc"
+KEYWORDS=""
+
+CDEPEND="sci-libs/libgenome
+ sci-libs/libmuscle
+ sci-libs/libmems"
+DEPEND="${CDEPEND}
+ doc? ( app-doc/doxygen )"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}"
+
+src_prepare() {
+ eautoreconf
+}
+
+src_install() {
+ emake install DESTDIR="${D}" || die
+}
diff --git a/sci-biology/mauvealigner/metadata.xml b/sci-biology/mauvealigner/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mauvealigner/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest
new file mode 100644
index 000000000000..88b4aef28107
--- /dev/null
+++ b/sci-biology/mcl/Manifest
@@ -0,0 +1,2 @@
+DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e
+DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279
diff --git a/sci-biology/mcl/mcl-08.312.ebuild b/sci-biology/mcl/mcl-08.312.ebuild
new file mode 100644
index 000000000000..9a2aafb0c037
--- /dev/null
+++ b/sci-biology/mcl/mcl-08.312.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ find \
+ -name Makefile.am \
+ -exec sed \
+ -e '/docdir/d' \
+ -e '/exampledir/s:doc::g' \
+ -i '{}' + || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=( $(use_enable blast) )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/mcl/mcl-12.135.ebuild b/sci-biology/mcl/mcl-12.135.ebuild
new file mode 100644
index 000000000000..9a2aafb0c037
--- /dev/null
+++ b/sci-biology/mcl/mcl-12.135.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ find \
+ -name Makefile.am \
+ -exec sed \
+ -e '/docdir/d' \
+ -e '/exampledir/s:doc::g' \
+ -i '{}' + || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=( $(use_enable blast) )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml
new file mode 100644
index 000000000000..aa6527e1e839
--- /dev/null
+++ b/sci-biology/mcl/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="blast">
+ add support for NCBI BLAST data
+ </flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
new file mode 100644
index 000000000000..3ed08610b06e
--- /dev/null
+++ b/sci-biology/meme/Manifest
@@ -0,0 +1 @@
+DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
new file mode 100644
index 000000000000..1293de0ea080
--- /dev/null
+++ b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
@@ -0,0 +1,17 @@
+--- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400
++++ Makefile.am 2007-04-24 10:37:37.000000000 -0400
+@@ -57,11 +57,11 @@
+ endif
+
+ dbdir:
+- mkdir -p $(MEME_DB)
++ mkdir -p $(DESTDIR)$(MEME_DB)
+
+ install-data-local:
+- mkdir -p $(MEME_LOGS)
+- chmod a+w $(MEME_LOGS)
++ mkdir -p $(DESTDIR)$(MEME_LOGS)
++ chmod a+w $(DESTDIR)$(MEME_LOGS)
+
+ distdir = $(PACKAGE)_$(VERSION)
+
diff --git a/sci-biology/meme/files/meme-3.5.4-patch1.patch b/sci-biology/meme/files/meme-3.5.4-patch1.patch
new file mode 100644
index 000000000000..b072d7edc527
--- /dev/null
+++ b/sci-biology/meme/files/meme-3.5.4-patch1.patch
@@ -0,0 +1,198 @@
+--- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000
++++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000
+@@ -1,6 +1,6 @@
+ #!@WHICHPERL@
+ ##
+-## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $
++## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $
+ ##
+ ## $Log: process_request.pl,v $
+ ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya
+@@ -55,7 +55,8 @@
+ $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl";
+ #
+ # You can change this if you wish to use a different JASPAR server
+-$jaspar_root = "http://mordor.cgb.ki.se";
++#$jaspar_root = "http://mordor.cgb.ki.se";
++$jaspar_root = "http://asp.ii.uib.no:8090";
+ $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl";
+ #
+ # You can change this if you wish to use a different Meta-MEME server
+@@ -221,7 +222,7 @@
+
+ $fasta = ""; # return value
+ @lines = split(/\n/, $block); # split block into lines
+- for ($i = 1; $i<$#lines; $i++) {
++ for ($i = 2; $i<$#lines; $i++) {
+ last if $lines[$i] =~ /^\/\//;
+ @words = split(/\s+/, $lines[$i]); # split line into words
+ # get sequence line
+@@ -239,7 +240,7 @@
+
+ $fasta = ""; # return value
+ @lines = split(/\n/, $block); # split block into lines
+- for ($i = 1; $i<$#lines; $i++) {
++ for ($i = 2; $i<$#lines; $i++) {
+ last if $lines[$i] =~ /^\/\//;
+ @words = split(/\s+/, $lines[$i]); # split line into words
+ # get id line and sequence line
+@@ -311,7 +312,8 @@
+ $content = $request->content;
+
+ # fix bug in JASPAR output; add database field to view buttons
+- $content =~ s/rm=present/rm=present&db=$sub_db/g;
++ # remove fix: JASPAR fixed the bug
++ # $content =~ s/rm=present/rm=present&db=$sub_db/g;
+
+ # display the page
+ print $content;
+--- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000
++++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000
+@@ -1,5 +1,5 @@
+ /*
+- * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $
++ * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $
+ *
+ * $Log$
+ * Revision 1.2 2006/03/08 20:50:11 nadya
+@@ -206,10 +206,9 @@
+
+ Local void addinfo(char *s, struct ReadSeqVars *V)
+ {
+- char s2[256], *si;
++ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char));
+ boolean saveadd;
+
+- si = s2;
+ while (*s == ' ') s++;
+ sprintf(si, " %d) %s\n", V->nseq, s);
+
+@@ -217,6 +216,7 @@
+ V->addit = true;
+ V->isseqchar = isAnyChar;
+ addseq( si, V);
++ free(si);
+ V->addit = saveadd;
+ V->isseqchar = isSeqChar;
+ }
+@@ -966,7 +966,6 @@
+ } while ((l == 0) && !feof(V->f));
+
+ if (feof(V->f)) V->err = eNoData;
+-
+ else switch (format_) {
+ case kPlain : readPlain(V); break;
+ case kIG : readIG(V); break;
+@@ -1181,7 +1180,7 @@
+ int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0;
+ char sp[MAXLINE];
+ long linestart=0;
+- int maxlines2check=500;
++ int maxlines2check=5000;
+
+ #define ReadOneLine(sp) \
+ { done |= (feof(fseq)); \
+--- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000
++++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000
+@@ -1,5 +1,5 @@
+ /*
+- * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $
++ * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $
+ *
+ * $Log$
+ * Revision 1.1 2005/07/29 19:12:07 nadya
+@@ -15,7 +15,7 @@
+ #include "config.h"
+ #include "macros.h"
+
+-#define MAXLINE 1024
++#define MAXLINE 10240
+
+ typedef char boolean;
+ #define NEWLINE '\n'
+--- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000
++++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000
+@@ -433,6 +433,7 @@
+ name[i++] = c; /* non-blank: add to name */
+ }
+ }
++ Resize(name, i+1, char);
+ name[i] = '\0';
+
+ /* read in description */
+--- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000
++++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000
+@@ -208,42 +208,39 @@
+ <h2><a name="patch">Getting and installing the patches</a></h2>
+ <p>The distribution may have patches associated with it. They are available
+ from <a href="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>.
+-The patch file name is <span class="command">filename.VERSION.patch</span>. In addition, a
+-patched file is distributed as well and can be used as a drop-in substitute
+-for the original file. The drop-in file is <span class="command">filename.VERSION</span>.
+-It is necessary to download only one of the two files depending on the method used for
+-patching. All patches for a specific version should be installed. The list
+-below provides instructions for installation of availble patches for specific
+-version.
++Patch files are located in a directory named
++<span class="command">VERSION.patches</span>,
++for example, <span class="command">meme_3.5.4.patches</span>.
++Patch file have names like:
++<span class="command">VERSION.patch_SERIAL_NO</span>, for example, <span class="command">meme_3.5.4.patch_3</span>.
++</p> <p> To install a patch, download the patch file from the URL given above.
++Then perform the following commands to install it:
++ <br><span class="command">$ cp PATCH_FILE VERSION </span> <br><span class="command">$ cd VERSION </span>
++ <br><span class="command">$ patch -p1 < PATCH_FILE </span>
++ <br><span class="command">$ make install </span>
++ <br><span class="command">$ make test </span>
++</p>
++<p>
++For example, to install the first patch to version meme_3.5.4, you would perform the following commands:
++ <br><span class="command">$ cp meme_3.5.4.patch_1 meme_3.5.4 </span>
++ <br><span class="command">$ cd meme_3.5.4 </span>
++ <br><span class="command">$ patch -p1 < meme_3.5.4.patch_1 </span>
++ <br><span class="command">$ make install </span>
++ <br><span class="command">$ make test </span>
++</p>
++<p>
++You must install all of the patches for a specific version in serial
++number order. For example, if you wish to install patch number 3,
++you must first have installed patches number 1 and 2 for that version.
++This is easy to do. Just download all the patches for your current
++version, copy them to your current versions's directory, and then
++install them in order by repeating the <span class="command">patch</span>,
++command above, with each patch file. You only need to run the
++<span class="command">install</span> and
++<span class="command">make test</span> commands once, after
++the last <span class="command">patch</patch> command.
+ </p>
+
+-<center>
+-<table class="large" border=1 cellspacing=0>
+-<tr>
+- <th width=7% class="head">Version</th>
+- <th width=25% class="head">Patch list</th>
+- <th class="head">Installation</th>
+-</tr>
+-<tr>
+- <td align=center>3.5.0</td>
+- <td align=center>mast-client.txt</td>
+- <td>
+- <ol>
+- <li>If downloaded a patch file <code>mast-client.txt.3.5.0.patch</code>:
+- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/</span>
+- <br><span class="command"># cd meme_3.5.0/scripts/</span>
+- <br><span class="command"># patch -p0 &lt; mast-client.txt.3.5.0.patch </span>
+- <br>
+- </li>
+- <li>If downloaded a patched file <code>mast-client.txt.3.5.0</code>:
+- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt</span>
+- </li>
+- </ol>
+- </td>
+-</tr>
+-</table>
+-</center>
+-
+ <p>
+ <p>[<a href="#top"> Top </a>]</p>
+
diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch
new file mode 100644
index 000000000000..cc07a98307f2
--- /dev/null
+++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch
@@ -0,0 +1,70 @@
+--- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000
++++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000
+@@ -1,6 +1,6 @@
+ #!@WHICHPERL@
+ ##
+-## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $
++## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $
+ ##
+ ## $Log$
+ ## Revision 1.12 2006/03/07 23:30:19 nadya
+@@ -467,21 +467,21 @@
+
+ # check against allowed dna letters
+ $x = $_;
+- $x =~ tr/ABCDGHKMNRSTUVWY//cd;
++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
+ $new = length $x;
+ if ($old == $new) {
+ "dna";
+ } else {
+ # check against allowed protein letters
+ $x = $_;
+- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
+ $new = length $x;
+ if ($old == $new) {
+ "protein";
+ } else {
+ # get the unknown letters
+ $x = $_;
+- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
+ &whine("
+ Your sequences contained the following unrecognized letters: $x.
+ <BR>
+--- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000
++++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000
+@@ -1,6 +1,6 @@
+ #!@WHICHPERL@
+ ##
+-## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $
++## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $
+ ##
+ ## $Log$
+ ## Revision 1.8 2006/03/07 23:30:19 nadya
+@@ -479,21 +479,21 @@
+
+ # check against allowed nucleotide letters
+ $x = $_;
+- $x =~ tr/ABCDGHKMNRSTUVWY//cd;
++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
+ $new = length $x;
+ if ($old == $new) {
+ return("DNA");
+ } else {
+ # check against allowed protein letters
+ $x = $_;
+- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
+ $new = length $x;
+ if ($old == $new) {
+ return("PROTEIN");
+ } else {
+ # get the unknown letters
+ $x = $_;
+- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
+ &whine("
+ Your sequences contained the following unrecognized letters: $x.
+ <BR>
diff --git a/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch
new file mode 100644
index 000000000000..1293de0ea080
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch
@@ -0,0 +1,17 @@
+--- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400
++++ Makefile.am 2007-04-24 10:37:37.000000000 -0400
+@@ -57,11 +57,11 @@
+ endif
+
+ dbdir:
+- mkdir -p $(MEME_DB)
++ mkdir -p $(DESTDIR)$(MEME_DB)
+
+ install-data-local:
+- mkdir -p $(MEME_LOGS)
+- chmod a+w $(MEME_LOGS)
++ mkdir -p $(DESTDIR)$(MEME_LOGS)
++ chmod a+w $(DESTDIR)$(MEME_LOGS)
+
+ distdir = $(PACKAGE)_$(VERSION)
+
diff --git a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
new file mode 100644
index 000000000000..e84006295735
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
@@ -0,0 +1,134 @@
+ Makefile.am | 6 +++---
+ doc/Makefile.am | 2 +-
+ doc/examples/Makefile.am | 24 +++++++++++-----------
+ .../Makefile.am | 2 +-
+ doc/examples/sample_opal_scripts/Makefile.am | 2 +-
+ doc/images/Makefile.am | 2 +-
+ scripts/Makefile.am | 2 +-
+ 7 files changed, 20 insertions(+), 20 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 4a69e34..842e33f 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -18,11 +18,11 @@ ARCHIVE_REVISION:
+ install-data-hook: dbdir
+
+ dbdir:
+- mkdir -p $(MEME_DB)
++ mkdir -p $(DESTDIR)$(MEME_DB)
+
+ install-data-local:
+- mkdir -p $(MEME_LOGS)
+- chmod a+w $(MEME_LOGS)
++ mkdir -p $(DESTDIR)$(MEME_LOGS)
++ chmod a+w $(DESTDIR)$(MEME_LOGS)
+
+ distdir = $(PACKAGE)_$(VERSION)
+
+diff --git a/doc/Makefile.am b/doc/Makefile.am
+index e0d6af9..e7bcb4f 100644
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -202,7 +202,7 @@ COMMON_DOC = \
+ if WEBSITE
+ MEME_DOC_DIR = $(WEBDIR)/doc
+ else
+-MEME_DOC_DIR = $(prefix)/doc
++MEME_DOC_DIR = $(docdir)/html
+ endif
+
+ memedocdir = $(MEME_DOC_DIR)
+diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am
+index 12970b5..633492c 100644
+--- a/doc/examples/Makefile.am
++++ b/doc/examples/Makefile.am
+@@ -51,24 +51,24 @@ if WEBSITE
+ exdir = $(WEBDIR)/examples
+ other_exdir = $(WEBDIR)/doc/examples
+ else
+-exdir = $(prefix)/doc/examples
++exdir = $(prefix)/share/meme/examples
+ other_exdir = $(exdir)
+ endif
+
+ ex_DATA = $(EXAMPLES)
+
+ install-data-hook:
+- tar xzvf centrimo_example_output_files.tgz -C $(other_exdir)
+- tar xzvf dreme_example_output_files.tgz -C $(other_exdir)
+- tar xzvf fimo_example_output_files.tgz -C $(other_exdir)
+- tar xzvf glam2_example_output_files.tgz -C $(other_exdir)
+- tar xzvf glam2scan_example_output_files.tgz -C $(other_exdir)
+- tar xzvf mast_example_output_files.tgz -C $(other_exdir)
+- tar xzvf mcast_example_output_files.tgz -C $(other_exdir)
+- tar xzvf meme_example_output_files.tgz -C $(other_exdir)
+- tar xzvf memechip_example_output_files.tgz -C $(other_exdir)
+- tar xzvf spamo_example_output_files.tgz -C $(other_exdir)
+- tar xzvf tomtom_example_output_files.tgz -C $(other_exdir)
++ tar xzvf centrimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf dreme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf fimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf glam2_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf glam2scan_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf mast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf mcast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf meme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf memechip_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf spamo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++ tar xzvf tomtom_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
+
+ # If .svnignore file doesn't exist
+ # create an empty one
+diff --git a/doc/examples/compute_prior_dist_example_output_files/Makefile.am b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
+index 747028d..a358f58 100644
+--- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
++++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
+@@ -22,7 +22,7 @@ EXAMPLES = \
+ if WEBSITE
+ exdir = $(WEBDIR)/doc/examples/compute_prior_dist_example_output_files
+ else
+-exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
++exdir = $(prefix)/share/meme/examples/compute_prior_dist_example_output_files
+ endif
+
+ ex_DATA = $(EXAMPLES)
+diff --git a/doc/examples/sample_opal_scripts/Makefile.am b/doc/examples/sample_opal_scripts/Makefile.am
+index 3a638b3..30925bb 100644
+--- a/doc/examples/sample_opal_scripts/Makefile.am
++++ b/doc/examples/sample_opal_scripts/Makefile.am
+@@ -18,7 +18,7 @@ EXAMPLES = \
+ if WEBSITE
+ exdir = $(WEBDIR)/doc/examples/sample_opal_scripts
+ else
+-exdir = $(prefix)/doc/examples/sample_opal_scripts
++exdir = $(prefix)/share/meme/examples/sample_opal_scripts
+ endif
+
+ ex_DATA = $(EXAMPLES)
+diff --git a/doc/images/Makefile.am b/doc/images/Makefile.am
+index c879621..a4696cd 100644
+--- a/doc/images/Makefile.am
++++ b/doc/images/Makefile.am
+@@ -28,7 +28,7 @@ MEME_IMAGES = \
+ if WEBSITE
+ memeimgdir = $(WEBDIR)/doc/images
+ else
+-memeimgdir = $(prefix)/doc/images
++memeimgdir = $(docdir)/html/images
+ endif
+
+ memeimg_DATA = $(MEME_IMAGES)
+diff --git a/scripts/Makefile.am b/scripts/Makefile.am
+index 4143e46..8a5c021 100644
+--- a/scripts/Makefile.am
++++ b/scripts/Makefile.am
+@@ -8,7 +8,7 @@
+ if WEBSITE
+ MEME_DOC_DIR = $(WEBDIR)/doc
+ else
+-MEME_DOC_DIR = $(prefix)/doc
++MEME_DOC_DIR = $(docdir)
+ endif
+
+ ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild
new file mode 100644
index 000000000000..8a1482c0b32d
--- /dev/null
+++ b/sci-biology/meme/meme-4.8.1-r2.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils python
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme.sdsc.edu/meme"
+SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
+
+LICENSE="meme"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="debug examples mpi"
+
+DEPEND="
+ app-shells/tcsh
+ dev-libs/libxml2:2
+ dev-libs/libxslt
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+#pkg_setup() {
+ # generate meme group to restrict logging to /var/log/meme
+# enewgroup meme
+# python_pkg_setup
+# python_set_active_version 2
+#}
+
+src_prepare() {
+ use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am
+ sed \
+ -e '/flags/s:-O3::g' \
+ -e '/opt/s:-O::g' \
+ -e '/debug/s:-ggdb::' \
+ -e '/debug/s:-g::' \
+ -e 's:CFLAGS=:CFLAGS+=:g' \
+ -i configure.ac || die
+ epatch \
+ "${FILESDIR}"/${P}-Makefile.am.patch
+ eautoreconf
+}
+
+src_configure() {
+ MY_PREFIX="${ROOT}opt/meme"
+ USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
+ econf \
+ --sysconfdir="${EPREFIX}/etc/meme" \
+ --with-logs="${ROOT}var/log/meme" \
+ $(use_enable debug) \
+ $USE_DISABLE_MPI
+}
+
+src_test() {
+ # bug #297070
+ emake -j1 test
+}
+
+src_install() {
+ local i
+ default
+
+ for i in "${ED}"/usr/bin/*; do
+ mv "${ED}"/usr/bin/{,meme-}$(basename ${i}) || die
+ done
+
+ echo "PATH=/opt/${PN}/bin" > 99${PN}
+ doenvd 99${PN}
+
+ # allow logging only for members of meme group
+ # diropts -m 0770 -g meme -o root
+ diropts -m ugo+rwxt -o root
+ keepdir /var/log/meme
+}
+
+#pkg_postinst() {
+# einfo 'Log files are produced in the "/var/log/meme" directory. Users'
+# einfo 'need to be part of the meme group to use this facility.'
+#}
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/meme/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml
new file mode 100644
index 000000000000..7a808874b6e6
--- /dev/null
+++ b/sci-biology/metadata.xml
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<catmetadata>
+ <longdescription lang="en">
+ The sci-biology category contains software that can be used
+ in biological and related scientific environments.
+ </longdescription>
+ <longdescription lang="de">
+ Die Kategorie sci-biology enthält Software, die in biologischen
+ und verwandten wissenschaftlichen Umgebungen genutzt werden kann.
+ </longdescription>
+ <longdescription lang="es">
+ La categoría sci-biology contiene programas que pueden ser utilizados en
+ entornos relacionados con la biología.
+ </longdescription>
+ <longdescription lang="ja">
+ sci-biologyカテゴリーには生物学の科学的な分野に利用される
+ ソフトウェアが含まれています。
+ </longdescription>
+ <longdescription lang="nl">
+ De sci-biology categorie bevat software, die in biologische en gerelateerde
+ wetenschappelijke omgevingen gebruikt kan worden.
+ </longdescription>
+ <longdescription lang="fr">
+ La catégorie sci-biology contient des logiciels pour les sciences
+ biologiques et les disciplines connexes.
+ </longdescription>
+ <longdescription lang="vi">
+ Nhóm sci-biology chứa các phần mềm sinh học và liên quan đến khoa học.
+ </longdescription>
+ <longdescription lang="sk">
+ Kategória sci-biology obsahuje programy, ktoré sa používajú pri
+ biologickom výskume.
+ </longdescription>
+ <longdescription lang="it">
+ La categoria sci-biology contiene programmi per la biologia.
+ </longdescription>
+ <longdescription lang="pt">
+ A categoria sci-biology contém programas que podem ser usados
+ em ambientes relacionados a biologia.
+ </longdescription>
+ <longdescription lang="pl">
+ Kategoria sci-biology zawiera programy naukowe związane z biologią.
+ </longdescription>
+</catmetadata>
+
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
new file mode 100644
index 000000000000..87d089e34446
--- /dev/null
+++ b/sci-biology/mira/Manifest
@@ -0,0 +1,2 @@
+DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747
+DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
new file mode 100644
index 000000000000..9bbd267cf4c8
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
@@ -0,0 +1,56 @@
+http://bugs.gentoo.org/show_bug.cgi?id=305547
+
+--- config/m4/ax_lib_expat.m4
++++ config/m4/ax_lib_expat.m4
+@@ -96,6 +99,7 @@
+
+ EXPAT_CFLAGS=""
+ EXPAT_LDFLAGS=""
++ EXPAT_LIBS=""
+ EXPAT_VERSION=""
+
+ dnl
+@@ -105,7 +109,8 @@
+
+ if test -n "$expat_prefix"; then
+ expat_include_dir="$expat_prefix/include"
+- expat_lib_flags="-L$expat_prefix/lib -lexpat"
++ expat_lib_flags="-L$expat_prefix/lib"
++ expat_libs="-lexpat"
+ run_expat_test="yes"
+ elif test "$expat_requested" = "yes"; then
+ if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
+@@ -126,6 +131,8 @@
+ saved_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $expat_lib_flags"
+
++ saved_LIBS="$LIBS"
++ LIBS="$LIBS $expat_libs"
+ dnl
+ dnl Check Expat headers
+ dnl
+@@ -171,7 +178,8 @@
+ ]]
+ )],
+ [
+ EXPAT_LDFLAGS="$expat_lib_flags"
++ EXPAT_LIBS="$expat_libs"
+ expat_lib_found="yes"
+ AC_MSG_RESULT([found])
+ ],
+@@ -185,6 +193,7 @@
+
+ CPPFLAGS="$saved_CPPFLAGS"
+ LDFLAGS="$saved_LDFLAGS"
++ LIBS="$saved_LIBS"
+ fi
+
+ AC_MSG_CHECKING([for Expat XML Parser])
+@@ -194,6 +203,7 @@
+
+ AC_SUBST([EXPAT_CFLAGS])
+ AC_SUBST([EXPAT_LDFLAGS])
++ AC_SUBST([EXPAT_LIBS])
+
+ HAVE_EXPAT="yes"
+ else
diff --git a/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
new file mode 100644
index 000000000000..27fb36467c8f
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
@@ -0,0 +1,52 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ src/examples_programming/Makefile.am | 2 +-
+ src/examples_programming/Makefile.in | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 3c4a999..a3bb19b 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+ for libextension in `ls $BOOSTLIBDIR/libboost_regex*.{so,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ if test "x$link_regex" != "xyes"; then
+ for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ fi
+diff --git a/src/examples_programming/Makefile.am b/src/examples_programming/Makefile.am
+index d77daaf..09c9965 100644
+--- a/src/examples_programming/Makefile.am
++++ b/src/examples_programming/Makefile.am
+@@ -11,7 +11,7 @@ AM_LDFLAGS= -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L..
+
+ mira_101.C:
+ mira_101_SOURCES= mira_101.C
+-mira_101_LDADD= -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD= -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+
+ read_101.C:
+ read_101_SOURCES= read_101.C
+diff --git a/src/examples_programming/Makefile.in b/src/examples_programming/Makefile.in
+index 27e6515..7dae4c4 100644
+--- a/src/examples_programming/Makefile.in
++++ b/src/examples_programming/Makefile.in
+@@ -222,7 +222,7 @@ AM_CXXFLAGS = $(BOOST_CPPFLAGS)
+ INCLUDES = -I$(top_srcdir)/src $(all_includes)
+ AM_LDFLAGS = -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf $(BOOST_LDFLAGS)
+ mira_101_SOURCES = mira_101.C
+-mira_101_LDADD = -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD = -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+ read_101_SOURCES = read_101.C
+ read_101_LDADD = -lmirasupport -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lm -lz
+ readpool_101_SOURCES = readpool_101.C
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
new file mode 100644
index 000000000000..427192294c81
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
@@ -0,0 +1,24 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 1ac06af..5b7be93 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+ for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ if test "x$link_regex" != "xyes"; then
+ for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ fi
diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
new file mode 100644
index 000000000000..14feb0284c9f
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cout.patch
@@ -0,0 +1,16 @@
+ src/progs/quirks.C | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/progs/quirks.C b/src/progs/quirks.C
+index 47e5ee8..060b6f3 100644
+--- a/src/progs/quirks.C
++++ b/src/progs/quirks.C
+@@ -25,6 +25,8 @@
+
+ #include <boost/filesystem.hpp>
+
++#include <iostream>
++
+ // make the "tcmalloc: large alloc" messages from TCMallom disappear
+ // by setting the reporting environment variable to a very large value
+ // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
new file mode 100644
index 000000000000..a2c7c1a0a6a7
--- /dev/null
+++ b/sci-biology/mira/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">mira-assembler</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
new file mode 100644
index 000000000000..3fa476c026a2
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
+
+inherit autotools eutils multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+ http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc"
+
+CDEPEND="
+ dev-libs/boost
+ dev-util/google-perftools"
+DEPEND="${CDEPEND}
+ app-editors/vim-core
+ dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+ epatch \
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
+ "${FILESDIR}"/${P}-cout.patch
+
+ sed \
+ -e "s:-O[23]::g" \
+ -e "s:-funroll-loops::g" \
+ -i configure.ac || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+# base_src_compile
+# # TODO: resolve docbook incompatibility for building docs
+# if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+ default
+ dodoc ${DOCS[@]}
+
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+ dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
new file mode 100644
index 000000000000..c71420fd1e4c
--- /dev/null
+++ b/sci-biology/mosaik/Manifest
@@ -0,0 +1,2 @@
+DIST Mosaik-1.0.1367-source.tar.bz2 8700231 SHA256 2a6ee1d25af835028b71f2518c6a00e929e64e7be6305183dfe0e242a015c750
+DIST Mosaik-1.0.1388-source.tar.bz2 8730164 SHA256 d6a8effa49adac617a388e2132aaf1a6b0679c783574d7df2cbd952a5f96e60c
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
new file mode 100644
index 000000000000..4dfd5b0bdafa
--- /dev/null
+++ b/sci-biology/mosaik/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="google-code">mosaik-aligner</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-1.0.1367.ebuild b/sci-biology/mosaik/mosaik-1.0.1367.ebuild
new file mode 100644
index 000000000000..f43c9b72ac37
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-1.0.1367.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}-source"
+
+src_compile() {
+ emake -C src || die
+# emake -C MosaikTools/c++ || die
+# emake -C MosaikTools/perl || die
+}
+
+src_install() {
+ dobin bin/* || die
+
+ insinto /usr/share/${PN}
+ doins -r MosaikTools || die
+
+ dodoc README Mosaik-1.0-Documentation.pdf
+}
diff --git a/sci-biology/mosaik/mosaik-1.0.1388.ebuild b/sci-biology/mosaik/mosaik-1.0.1388.ebuild
new file mode 100644
index 000000000000..4c9664caa80a
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-1.0.1388.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/mosaik-aligner"
+
+src_prepare() {
+ sed -i 's/-static//' src/includes/linux.inc || die
+}
+
+src_compile() {
+ emake -C src || die
+# emake -C MosaikTools/c++ || die
+# emake -C MosaikTools/perl || die
+}
+
+src_install() {
+ dobin bin/* || die
+
+ insinto /usr/share/${PN}
+ doins -r MosaikTools || die
+
+ dodoc README Mosaik-1.0-Documentation.pdf
+}
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
new file mode 100644
index 000000000000..e0cf36aefaf6
--- /dev/null
+++ b/sci-biology/mothur/Manifest
@@ -0,0 +1,2 @@
+DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361
+DIST mothur-1.6.0.zip 465292 SHA256 75583a204d199ddcf9b845fc0adbaf240d7b1f08584fed5e6465982f68ffe121 SHA512 f775ff64991f00423108f295eca640f5c5d85a38e01b31af44ddf91f8897968e934f79899a21606dfd81fdc3e91751df277237e94d56d74f862e472e8da3386c WHIRLPOOL 31ca8decceb38ebd17f15c5f937df70b501833311cbf1aec794bb174d409a0c01e77abb399347781ad820c06411e56c566382a32818a0c57214aad2ad16cc132
diff --git a/sci-biology/mothur/files/mothur-1.27.0-makefile.patch b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch
new file mode 100644
index 000000000000..52a02585df14
--- /dev/null
+++ b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch
@@ -0,0 +1,52 @@
+ makefile | 14 ++++++--------
+ 1 files changed, 6 insertions(+), 8 deletions(-)
+
+diff --git a/makefile b/makefile
+index db7c904..109488f 100644
+--- a/makefile
++++ b/makefile
+@@ -10,18 +10,18 @@
+ #
+
+ USEMPI ?= no
+-64BIT_VERSION ?= yes
++64BIT_VERSION ?= no
+ USEREADLINE ?= yes
+ CYGWIN_BUILD ?= no
+ USECOMPRESSION ?= no
+ MOTHUR_FILES="\"Enter_your_default_path_here\""
+ RELEASE_DATE = "\"8/8/2012\""
+ VERSION = "\"1.27.0\""
+-FORTAN_COMPILER = gfortran
+-FORTRAN_FLAGS =
++FORTAN_COMPILER = ${FC}
++FORTRAN_FLAGS = ${FCFLAGS}
+
+ # Optimize to level 3:
+-CXXFLAGS += -O3
++#CXXFLAGS += -O3
+
+ ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
+@@ -69,7 +69,7 @@ endif
+
+
+ ifeq ($(strip $(USEMPI)),yes)
+- CXX = mpic++
++# CXX = mpic++
+ CXXFLAGS += -DUSE_MPI
+ endif
+
+@@ -95,11 +95,9 @@ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+ OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+
+-mothur : fortranSource $(OBJECTS) uchime
++mothur : fortranSource $(OBJECTS)
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+
+- strip mothur
+-
+ uchime:
+ cd uchime_src && ./mk && mv uchime .. && cd ..
+
diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch
new file mode 100644
index 000000000000..0b612cf7b529
--- /dev/null
+++ b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch
@@ -0,0 +1,93 @@
+ chimerauchimecommand.cpp | 2 +-
+ clearcutcommand.cpp | 32 ++++++++++++++++----------------
+ 2 files changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
+index bd31c19..2070840 100644
+--- a/chimerauchimecommand.cpp
++++ b/chimerauchimecommand.cpp
+@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
+ }
+
+ if (ucl) {
+- char* tempucl = new char[5];
++ char* tempucl = new char[6];
+ strcpy(tempucl, "--ucl");
+ cPara.push_back(tempucl);
+ }
+diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
+index 6a0eb25..2e8164e 100644
+--- a/clearcutcommand.cpp
++++ b/clearcutcommand.cpp
+@@ -269,35 +269,35 @@ int ClearcutCommand::execute() {
+
+ vector<char*> cPara;
+
+- char* tempClearcut = new char[8];
++ char* tempClearcut = new char[16];
+ strcpy(tempClearcut, "clearcut");
+ cPara.push_back(tempClearcut);
+
+ //you gave us a distance matrix
+- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
++ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); }
+
+ //you gave us a fastafile
+- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
++ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
+
+- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
+- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
+- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
++ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); }
++ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
++ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
+ if (seed != "*") {
+ string tempSeed = "--seed=" + seed;
+ char* temp = new char[tempSeed.length()];
+ strcpy(temp, tempSeed.c_str());
+ cPara.push_back(temp);
+ }
+- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
+- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
+- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
++ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
++ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
++ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
+
+ string tempIn = "--in=" + inputFile;
+ char* tempI = new char[tempIn.length()];
+ strcpy(tempI, tempIn.c_str());
+ cPara.push_back(tempI);
+
+- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
++ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
+ else{
+ string tempOut = "--out=" + outputName;
+
+@@ -306,10 +306,10 @@ int ClearcutCommand::execute() {
+ cPara.push_back(temp);
+ }
+
+- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
+- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
+- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
+- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
++ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
++ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); }
++ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
++ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
+ if (matrixout != "") {
+ string tempMatrix = "--matrixout=" + outputDir + matrixout;
+ char* temp = new char[tempMatrix.length()];
+@@ -326,8 +326,8 @@ int ClearcutCommand::execute() {
+ cPara.push_back(temp);
+ }
+
+- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
+- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
++ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
++ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
+
+ char** clearcutParameters;
+ clearcutParameters = new char*[cPara.size()];
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mothur/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
new file mode 100644
index 000000000000..3de23de65d51
--- /dev/null
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite of algorithms for ecological bioinformatics"
+HOMEPAGE="http://www.mothur.org/"
+SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="mpi +readline"
+KEYWORDS="amd64 ~x86"
+
+RDEPEND="
+ sci-biology/uchime
+ mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}
+ app-arch/unzip"
+
+S=${WORKDIR}/Mothur.source
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
+ use amd64 && append-cppflags -DBIT_VERSION
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-makefile.patch \
+ "${FILESDIR}"/${P}-overflows.patch
+}
+
+src_compile() {
+ emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline)
+}
+
+src_install() {
+ dobin ${PN}
+}
diff --git a/sci-biology/mothur/mothur-1.6.0.ebuild b/sci-biology/mothur/mothur-1.6.0.ebuild
new file mode 100644
index 000000000000..034f6fae1a65
--- /dev/null
+++ b/sci-biology/mothur/mothur-1.6.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="A suite of algorithms for ecological bioinformatics"
+HOMEPAGE="http://www.mothur.org/"
+SRC_URI="mirror://gentoo/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+S="${WORKDIR}/mothur-v.${PV}"
+
+src_prepare() {
+ sed \
+ -e 's/CC_OPTIONS =.*$/CC_OPTIONS = ${CXXFLAGS} /' \
+ -e 's|CC = g++|CC = '$(tc-getCXX)'|' \
+ -e '/^LNK_OPTIONS/s:$:${LDFLAGS}:g' \
+ -i makefile || die
+}
+
+src_install() {
+ dobin ${PN}
+}
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
new file mode 100644
index 000000000000..d932da527753
--- /dev/null
+++ b/sci-biology/mrbayes/Manifest
@@ -0,0 +1 @@
+DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f
diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch
new file mode 100644
index 000000000000..2f8bab1e7665
--- /dev/null
+++ b/sci-biology/mrbayes/files/mb_readline_312.patch
@@ -0,0 +1,37 @@
+Index: Makefile
+===================================================================
+RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v
+retrieving revision 3.23
+retrieving revision 3.24
+diff -U2 -r3.23 -r3.24
+--- Makefile 22 Dec 2005 16:13:06 -0000 3.23
++++ Makefile 3 Jan 2006 16:43:13 -0000 3.24
+@@ -50,4 +50,5 @@
+ ifeq ($(strip $(USEREADLINE)),yes)
+ CFLAGS += -DUSE_READLINE
++# CFLAGS += -DCOMPLETIONMATCHES
+ LIBS += -lncurses -lreadline
+ endif
+Index: bayes.c
+===================================================================
+RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v
+retrieving revision 3.39
+retrieving revision 3.40
+diff -U2 -r3.39 -r3.40
+--- bayes.c 23 Dec 2005 16:26:28 -0000 3.39
++++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40
+@@ -382,9 +382,11 @@
+ char **readline_completion(const char *text, int start, int stop) {
+ char **matches = (char **) NULL;
+-
++
++#ifdef COMPLETIONMATCHES
+ if(start == 0)
+- matches = rl_completion_matches (text, command_generator);
++ matches = rl_completion_matches (text, command_generator);
++#endif
+
+- return (matches);
++ return (matches);
+ }
+ #endif
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
new file mode 100644
index 000000000000..8a6a5b986dc7
--- /dev/null
+++ b/sci-biology/mrbayes/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+MrBayes is a program for the Bayesian estimation of phylogeny.
+Bayesian inference of phylogeny is based upon a quantity called the
+posterior probability distribution of trees, which is the probability of a
+tree conditioned on the observations. The conditioning is accomplished using
+Bayes's theorem. The posterior probability distribution of trees is
+impossible to calculate analytically; instead, MrBayes uses a simulation
+technique called Markov chain Monte Carlo (or MCMC) to approximate the
+posterior probabilities of trees.
+</longdescription>
+ <upstream>
+ <remote-id type="sourceforge">mrbayes</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
new file mode 100644
index 000000000000..b4303b8f90b3
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://mrbayes.csit.fsu.edu/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="debug mpi readline"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="
+ sys-libs/ncurses
+ mpi? ( virtual/mpi )
+ readline? ( sys-libs/readline:0 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ use readline && epatch "${FILESDIR}"/mb_readline_312.patch
+ sed -e 's:-ggdb::g' -i Makefile || die
+}
+
+src_compile() {
+ local myconf mycc
+
+ if use mpi; then
+ mycc=mpicc
+ else
+ mycc=$(tc-getCC)
+ fi
+
+ use mpi && myconf="MPI=yes"
+ use readline || myconf="${myconf} USEREADLINE=no"
+ use debug && myconf="${myconf} DEBUG=yes"
+ emake \
+ OPTFLAGS="${CFLAGS}" \
+ LDFLAGS="${LDFLAGS}" \
+ CC=${mycc} \
+ ${myconf}
+}
+
+src_install() {
+ dobin mb
+ insinto /usr/share/${PN}
+ doins *.nex
+}
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
new file mode 100644
index 000000000000..0c5a5015ecc7
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://mrbayes.csit.fsu.edu/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="debug mpi readline"
+
+DEPEND="
+ sys-libs/ncurses
+ mpi? ( virtual/mpi )
+ readline? ( sys-libs/readline:0= )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ if use mpi; then
+ sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support."
+ fi
+ if ! use readline; then
+ sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \
+ -i Makefile || die "Patching readline support."
+ else
+ # Only needed for OSX with an old (4.x) version of
+ # libreadline, but it doesn't hurt for other distributions.
+ epatch "${FILESDIR}"/mb_readline_312.patch
+ fi
+ sed -e 's:-ggdb::g' -i Makefile || die
+}
+
+src_compile() {
+ local myconf mycc
+
+ if use mpi; then
+ mycc=mpicc
+ else
+ mycc=$(tc-getCC)
+ fi
+
+ use mpi && myconf="MPI=yes"
+ use readline || myconf="${myconf} USEREADLINE=no"
+ use debug && myconf="${myconf} DEBUG=yes"
+ emake \
+ OPTFLAGS="${CFLAGS}" \
+ LDFLAGS="${LDFLAGS}" \
+ CC=${mycc} \
+ ${myconf}
+}
+
+src_install() {
+ dobin mb
+ insinto /usr/share/${PN}
+ doins *.nex
+}
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
new file mode 100644
index 000000000000..bae1ccf2f14c
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,3 @@
+DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260
+DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8
+DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da
diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch
new file mode 100644
index 000000000000..d3c4a60a1adb
--- /dev/null
+++ b/sci-biology/mummer/files/3.22-ldflags.patch
@@ -0,0 +1,16 @@
+diff --git a/src/tigr/Makefile b/src/tigr/Makefile
+index cf6b9ca..5b28d1e 100644
+--- a/src/tigr/Makefile
++++ b/src/tigr/Makefile
+@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR)
+ endif
+
+ OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
+-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
++BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
+ chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
++AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+ chmod 755 $(AUX_BIN_DIR)/$@
+ VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+
diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch
new file mode 100644
index 000000000000..3b24ee40214a
--- /dev/null
+++ b/sci-biology/mummer/files/3.22-prll.patch
@@ -0,0 +1,56 @@
+diff --git a/Makefile b/Makefile
+index 4db4977..bbd00ed 100644
+--- a/Makefile
++++ b/Makefile
+@@ -114,15 +114,15 @@ install: all
+
+
+ kurtz:
+- cd $(KURTZ_SRC_DIR); $(MAKE) mummer
++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer
+
+
+ scripts:
+- cd $(SCRIPT_DIR); $(MAKE) all
++ $(MAKE) -C $(SCRIPT_DIR) all
+
+
+ tigr:
+- cd $(TIGR_SRC_DIR); $(MAKE) all
++ $(MAKE) -C $(TIGR_SRC_DIR) all
+
+
+ uninstall: clean
+diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile
+index 85dfc16..5bff793 100644
+--- a/src/kurtz/Makefile
++++ b/src/kurtz/Makefile
+@@ -1,7 +1,7 @@
+ all:
+- cd libbasedir; $(MAKE) all
+- cd streesrc; $(MAKE) all
+- cd mm3src; $(MAKE) all
++ $(MAKE) -C libbasedir all
++ $(MAKE) -C streesrc all
++ $(MAKE) -C mm3src all
+
+ clean:
+ rm -f *~
+@@ -10,11 +10,11 @@ clean:
+ cd mm3src; $(MAKE) clean
+
+ mummer:
+- cd libbasedir; $(MAKE) libbase.a
+- cd streesrc; $(MAKE) libstree.a
+- cd mm3src; $(MAKE) mummer
++ $(MAKE) -C libbasedir libbase.a
++ $(MAKE) -C streesrc libstree.a
++ $(MAKE) -C mm3src mummer
+
+ splintall:
+- cd libbasedir; ${MAKE} splintall
+- cd streesrc; ${MAKE} splintall
+- cd mm3src; ${MAKE} splintall
++ $(MAKE) -C libbasedir splintall
++ $(MAKE) -C streesrc splintall
++ $(MAKE) -C mm3src splintall
diff --git a/sci-biology/mummer/files/mummer-3.20-gcc43.patch b/sci-biology/mummer/files/mummer-3.20-gcc43.patch
new file mode 100644
index 000000000000..4d3edb41e46a
--- /dev/null
+++ b/sci-biology/mummer/files/mummer-3.20-gcc43.patch
@@ -0,0 +1,12 @@
+--- src/tigr/show-diff.cc.orig 2008-06-16 17:55:34.000000000 +0000
++++ src/tigr/show-diff.cc 2008-06-16 17:56:25.000000000 +0000
+@@ -14,6 +14,8 @@
+ #include <cstdlib>
+ #include <cassert>
+ #include <climits>
++#include <algorithm>
++
+ using namespace std;
+
+
+
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
new file mode 100644
index 000000000000..f82b462e1f95
--- /dev/null
+++ b/sci-biology/mummer/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">mummer</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild
new file mode 100644
index 000000000000..2f566667ceca
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.20.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils
+
+MY_P="MUMmer${PV}"
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-gcc43.patch
+ # Warning: package uses CPPFLAGS on c in addition to cpp, despite the name
+ sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
+ -e 's/LDFLAGS =$//' "${S}/Makefile"
+}
+
+src_compile() {
+ emake || die "emake failed"
+
+ sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ -e 's|\(set bindir = \).*|\1/usr/bin|' \
+ -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+ -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
+ sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+ dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+ exact-tandems promer repeat-match show-aligns gaps mummer \
+ show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die
+ newbin annotate mummer-annotate || die
+
+ insinto /usr/share/${PN}/scripts
+ doins scripts/{*.awk,*.csh,*.pl}
+ insinto /usr/share/${PN}/lib
+ doins scripts/Foundation.pm || die
+
+ dodoc ACKNOWLEDGEMENTS ChangeLog README
+ insinto /usr/share/doc/${PF}
+ use doc && doins -r docs
+}
diff --git a/sci-biology/mummer/mummer-3.21.ebuild b/sci-biology/mummer/mummer-3.21.ebuild
new file mode 100644
index 000000000000..64eaf1b3646a
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.21.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils
+
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/MUMmer${PV}"
+
+src_unpack() {
+ unpack ${A}
+ # Warning: package uses CPPFLAGS on c as well as cpp, despite the name
+ sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
+ -e 's/LDFLAGS =$//' "${S}/Makefile" || die
+}
+
+src_compile() {
+ emake || die
+
+ sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ -e 's|\(set bindir = \).*|\1/usr/bin|' \
+ -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+ -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
+ mv annotate mummer-annotate || die
+ sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
+}
+
+src_install() {
+ dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
+
+ insinto /usr/share/${PN}/scripts
+ doins scripts/{*.awk,*.csh,*.pl} || die
+ insinto /usr/share/${PN}/lib
+ doins scripts/Foundation.pm || die
+
+ dodoc ACKNOWLEDGEMENTS ChangeLog README
+ insinto /usr/share/doc/${PF}
+ use doc && doins -r docs
+}
diff --git a/sci-biology/mummer/mummer-3.22-r1.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild
new file mode 100644
index 000000000000..ad60acce35a4
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.22-r1.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit eutils flag-o-matic
+
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/MUMmer${PV}"
+
+src_prepare() {
+ use amd64 && append-flags -DSIXTYFOURBITS
+
+ epatch \
+ "${FILESDIR}"/${PV}-prll.patch \
+ "${FILESDIR}"/${PV}-ldflags.patch
+
+ sed \
+ -e '/^CFLAGS/d' \
+ -e '/^CXXFLAGS/d' \
+ -e '/^LDFLAGS/d' \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake || die
+
+ sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+ -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ -e 's|\(set bindir = \).*|\1/usr/bin|' \
+ -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+ -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+ scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
+ mv annotate mummer-annotate || die
+ sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
+}
+
+src_install() {
+ dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die
+
+ insinto /usr/share/${PN}/scripts
+ doins scripts/{*.awk,*.csh,*.pl} || die
+ insinto /usr/share/${PN}/lib
+ doins scripts/Foundation.pm || die
+
+ dodoc ACKNOWLEDGEMENTS ChangeLog README || die
+ insinto /usr/share/doc/${PF}
+ if use doc; then
+ doins -r docs || die
+ fi
+}
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
new file mode 100644
index 000000000000..2dbd476bb5b4
--- /dev/null
+++ b/sci-biology/muscle/Manifest
@@ -0,0 +1 @@
+DIST muscle3.8.31_src.tar.gz 515267 SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce WHIRLPOOL daea88aaeaaacf5a2da68484010091ae46c69713659f92f45e5e2096af9e7d8c645d14e5b6c4c8e73e4df35a086dee823fcab6d442cd3881b773fb0113ce897d
diff --git a/sci-biology/muscle/files/3.7-bufferoverflow.patch b/sci-biology/muscle/files/3.7-bufferoverflow.patch
new file mode 100644
index 000000000000..670ad64959cb
--- /dev/null
+++ b/sci-biology/muscle/files/3.7-bufferoverflow.patch
@@ -0,0 +1,26 @@
+diff --git a/globalslinux.cpp b/globalslinux.cpp
+index 63baaa1..b1cfcb0 100644
+--- a/globalslinux.cpp
++++ b/globalslinux.cpp
+@@ -156,7 +156,7 @@ double GetRAMSizeMB()
+ }
+ return DEFAULT_RAM;
+ }
+- int Bytes = atoi(pMem+9)*1000;
++ long Bytes = atol(pMem+9)*1000;
+ return ((double) Bytes)/1e6;
+ }
+
+diff --git a/progress.cpp b/progress.cpp
+index a0e91bb..f9b093e 100644
+--- a/progress.cpp
++++ b/progress.cpp
+@@ -41,7 +41,7 @@ const char *MemToStr(double MB)
+ if (MB < 0)
+ return "";
+
+- static char Str[9];
++ static char Str[16];
+ static double MaxMB = 0;
+ static double RAMMB = 0;
+
diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch
new file mode 100644
index 000000000000..7c0e7308df54
--- /dev/null
+++ b/sci-biology/muscle/files/3.8.31-make.patch
@@ -0,0 +1,26 @@
+diff --git a/src/mk b/src/mk
+index 475d25a..d4b7e83 100755
+--- a/src/mk
++++ b/src/mk
+@@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln
+ rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
+ for CPPName in $CPPNames
+ do
+- echo $CPPName >> /dev/tty
+- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++ echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o"
++ ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o
+ done
+
+ LINK_OPTS=
+ if [ `uname -s` == Linux ] ; then
+ LINK_OPTS=-static
+ fi
+-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+-tail muscle.make.stderr.txt
+
+-strip muscle
+-ls -lh muscle
+-sum muscle
++echo "${CXX} ${LDFLAGS} -o muscle $ObjNames"
++${CXX} ${LDFLAGS} -o muscle $ObjNames
diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/muscle/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
new file mode 100644
index 000000000000..555419da883f
--- /dev/null
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}${PV}_src"
+
+DESCRIPTION="Multiple sequence comparison by log-expectation"
+HOMEPAGE="http://www.drive5.com/muscle/"
+SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE=""
+
+RDEPEND="!sci-libs/libmuscle"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}${PV}/src
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-make.patch
+ tc-export CXX
+}
+
+src_install() {
+ dobin "${PN}"
+ dodoc *.txt
+}
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
new file mode 100644
index 000000000000..b4e27e229585
--- /dev/null
+++ b/sci-biology/ncbi-tools/Manifest
@@ -0,0 +1 @@
+DIST ncbi-tools-2.2.26.tar.gz 68691452 SHA256 d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 WHIRLPOOL 6f390a4487b7ebf9d5ca31018f3b33602a695e4b0a4b090952fec9c7e8c3956edc197e75ffd32588f9431cc04b4262a2ca2e3b0ba50dd622ed73a4da6655a956
diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1
new file mode 100644
index 000000000000..d4de68e6081a
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/21ncbi-r1
@@ -0,0 +1,6 @@
+# Location of the formatdb data sets
+BLASTDB="/usr/share/ncbi/formatdb"
+# Location of the BLAST matrixes.
+BLASTMAT="/usr/share/ncbi/data"
+# Location of the ".ncbi.rc" file which sets the default path for shared data.
+NCBI=/etc/ncbi
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
new file mode 100644
index 000000000000..bbc4623609c8
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
@@ -0,0 +1,81 @@
+ corelib/ncbilcl.beos | 2 +-
+ corelib/ncbilcl.hlx | 2 +-
+ corelib/ncbilcl.lnx | 4 ++--
+ corelib/ncbilcl.plx | 2 +-
+ corelib/ncbilcl.qnx | 2 +-
+ 5 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos
+index f720567..fe6346f 100644
+--- a/corelib/ncbilcl.beos
++++ b/corelib/ncbilcl.beos
+@@ -77,7 +77,7 @@
+ #endif
+
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+
+
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx
+index 1492f93..0e98fb6 100644
+--- a/corelib/ncbilcl.hlx
++++ b/corelib/ncbilcl.hlx
+@@ -67,7 +67,7 @@
+ #endif
+
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-/*#define _SVID_SOURCE 1 */
++/*#define _DEFAULT_SOURCE 1 */
+
+
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
+index 46e2978..b3256b3 100644
+--- a/corelib/ncbilcl.lnx
++++ b/corelib/ncbilcl.lnx
+@@ -65,7 +65,7 @@
+ * fixes for new RedHat6.2
+ *
+ * Revision 6.3 2000/02/10 16:36:32 vakatov
+-* Added _SVID_SOURCE
++* Added _DEFAULT_SOURCE
+ *
+ * Revision 6.2 1999/07/12 05:50:49 vakatov
+ * Avoid redefinition of #_REENTRANT
+@@ -141,7 +141,7 @@
+ #endif
+
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+ #define _GNU_SOURCE 1
+
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx
+index bf5824c..f2b53e1 100644
+--- a/corelib/ncbilcl.plx
++++ b/corelib/ncbilcl.plx
+@@ -68,7 +68,7 @@
+ #endif
+
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-/*#define _SVID_SOURCE 1 */
++/*#define _DEFAULT_SOURCE 1 */
+
+
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx
+index c3d1f0a..4b27bd1 100644
+--- a/corelib/ncbilcl.qnx
++++ b/corelib/ncbilcl.qnx
+@@ -72,7 +72,7 @@
+ #endif
+
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+
+
+
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
new file mode 100644
index 000000000000..e6763214a6e5
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
@@ -0,0 +1,103 @@
+ cdromlib/cdnewlib.c | 6 +++---
+ corelib/ncbierr.c | 2 +-
+ corelib/ncbisgml.c | 8 ++++----
+ demo/errhdr.c | 2 +-
+ 4 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c
+index 461292c..be4a2d6 100644
+--- a/cdromlib/cdnewlib.c
++++ b/cdromlib/cdnewlib.c
+@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi
+ char volname[16];
+ volname[0] = '\0';
+ if (cddev->volume != NULL)
+- strncat(volname,cddev->volume->volume_name,sizeof volname);
++ strncat(volname,cddev->volume->volume_name,sizeof volname - 1);
+ else
+ sprintf(volname,"entrez%d",cddev->hint);
+ if (!FileBuildPath(fpath,volname,NULL))
+@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev)
+ memset((void*)&info,0,sizeof info);
+ fpath[0] = '\0';
+ if (cddev->inf.root !=NULL)
+- strncat(fpath,cddev->inf.root,sizeof fpath);
++ strncat(fpath,cddev->inf.root,sizeof fpath - 1);
+
+ if (cddev->ins_volname)
+ {
+@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev)
+ {
+ fpath[0] = '\0';
+ if (cddev->inf.root !=NULL)
+- strncat(fpath,cddev->inf.root,sizeof fpath);
++ strncat(fpath,cddev->inf.root,sizeof fpath - 1);
+ sprintf(volname,"entrez%d",j+1);
+ FileBuildPath(fpath,volname,NULL);
+ if (CdTestPath(fpath,&info))
+diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
+index 0429d86..7b96a2e 100644
+--- a/corelib/ncbierr.c
++++ b/corelib/ncbierr.c
+@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx)
+ if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL)
+ {
+ strcpy(path,info->msgpath);
+- strncat(path,file,sizeof(path));
++ strncat(path,file,sizeof(path) - 1);
+ fd = FileOpen(path,s_msg_mode);
+ }
+
+diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c
+index 99412be..a653aef 100644
+--- a/corelib/ncbisgml.c
++++ b/corelib/ncbisgml.c
+@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
+ }
+ if (i >= num_sgml_entity)
+ {
+- char bad[SGML_ERROR_MSG_LIM];
++ char bad[SGML_ERROR_MSG_LIM + 2];
+ bad[0] = '\0';
+ strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
+@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
+ from++;
+ if (*from == '\0')
+ {
+- char bad[SGML_ERROR_MSG_LIM];
++ char bad[SGML_ERROR_MSG_LIM + 2];
+ bad[0] = '\0';
+ strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad);
+@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml)
+ }
+ if (i >= num_sgml_entity)
+ {
+- char bad[SGML_ERROR_MSG_LIM];
++ char bad[SGML_ERROR_MSG_LIM + 2];
+ bad[0] = '\0';
+ strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
+@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml)
+ from++;
+ if (*from == '\0')
+ {
+- char bad[SGML_ERROR_MSG_LIM];
++ char bad[SGML_ERROR_MSG_LIM + 2];
+ bad[0] = '\0';
+ strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad);
+diff --git a/demo/errhdr.c b/demo/errhdr.c
+index 01cd955..5081489 100644
+--- a/demo/errhdr.c
++++ b/demo/errhdr.c
+@@ -41,7 +41,7 @@ int main (int argc, char **argv)
+ else if (mod[0] == '\0')
+ {
+ char *p;
+- strncat(mod,argv[i],sizeof mod);
++ strncat(mod,argv[i],sizeof mod - 1);
+ if ((p = strstr(argv[i],".msg")) != NULL)
+ *p = '\0';
+ }
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
new file mode 100644
index 000000000000..c12feff51af1
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
@@ -0,0 +1,124 @@
+ api/alignmgr2.c | 2 +-
+ api/pgppop.c | 2 +-
+ api/txalign.c | 10 +++++-----
+ desktop/seqpanel.c | 4 ++--
+ tools/spidey.c | 4 ++--
+ 5 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/api/alignmgr2.c b/api/alignmgr2.c
+index 5b43ef3..4b9007e 100644
+--- a/api/alignmgr2.c
++++ b/api/alignmgr2.c
+@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn
+ spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode);
+ ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1);
+ buf[ctr] = '\0';
+- fprintf(ofp, buf);
++ fprintf(ofp, "%s", buf);
+ SeqPortFree(spp);
+ }
+ }
+diff --git a/api/pgppop.c b/api/pgppop.c
+index d16d79d..b359378 100644
+--- a/api/pgppop.c
++++ b/api/pgppop.c
+@@ -2994,7 +2994,7 @@ Char DefLine[255];
+ if (szSeq){
+ if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL,
+ NULL,NULL)) continue;
+- fprintf(fp,szSeq);
++ fprintf(fp, "%s", szSeq);
+ fprintf(fp,"\n");
+ MemFree(szSeq);
+ }
+diff --git a/api/txalign.c b/api/txalign.c
+index 5877f9c..cb35fbc 100644
+--- a/api/txalign.c
++++ b/api/txalign.c
+@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
+ Char checkboxBuf[200];
+ sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
+- sprintf(docbuf+pos,checkboxBuf);
++ sprintf(docbuf+pos,"%s", checkboxBuf);
+
+ pos += StringLen(checkboxBuf);
+ }
+
+ html_len = StringLen(HTML_buffer);
+- sprintf(docbuf+pos, HTML_buffer);
++ sprintf(docbuf+pos, "%s", HTML_buffer);
+ pos += html_len;
+
+ pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
+@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id);
+
+ html_len = StringLen(HTML_buffer);
+- sprintf(docbuf+pos, HTML_buffer);
++ sprintf(docbuf+pos, "%s", HTML_buffer);
+ pos += html_len;
+ pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
+ tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
+@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id);
+
+ html_len = StringLen(HTML_buffer);
+- sprintf(docbuf+pos, HTML_buffer);
++ sprintf(docbuf+pos, "%s", HTML_buffer);
+ pos += html_len;
+ pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
+ tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
+@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
+ Char checkboxBuf[200];
+ sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb);
+- sprintf(docbuf+pos,checkboxBuf);
++ sprintf(docbuf+pos,"%s",checkboxBuf);
+
+ pos += StringLen(checkboxBuf);
+ }
+diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
+index 2e78e13..c7538aa 100644
+--- a/desktop/seqpanel.c
++++ b/desktop/seqpanel.c
+@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx
+ seqbuf, alnbuf, &alnbuf_len,
+ show_substitutions);
+ MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len);
+- fprintf (fp, printed_line);
++ fprintf (fp, "%s", printed_line);
+ }
+ fprintf (fp, "\n");
+ start = stop + 1;
+@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile
+ seqbuf, alnbuf, &alnbuf_len,
+ show_substitutions);
+ MemCpy (printed_line, alnbuf, alnbuf_len);
+- fprintf (fp, printed_line);
++ fprintf (fp, "%s", printed_line);
+ start = stop + 1;
+ stop += seq_chars_per_row;
+ }
+diff --git a/tools/spidey.c b/tools/spidey.c
+index d6ce62d..ac9f59a 100644
+--- a/tools/spidey.c
++++ b/tools/spidey.c
+@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose
+ fprintf(ofp2, " ");
+ ctr++;
+ }
+- fprintf(ofp2, buf);
++ fprintf(ofp2, "%s", buf);
+ if (spp){
+ SeqPortFree(spp);
+ }
+@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S
+ ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10);
+ if (ctr > 0)
+ buf[ctr] = '\0';
+- fprintf(ofp2, buf);
++ fprintf(ofp2, "%s", buf);
+ SeqPortFree(spp);
+ }
+ done = TRUE;
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
new file mode 100644
index 000000000000..1cd7976af599
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
@@ -0,0 +1,27 @@
+--- ncbi-20050605/make/makedis.csh 2005-05-13 05:42:12.000000000 +0200
++++ ncbi/make/makedis.csh 2005-09-20 22:02:38.000000000 +0200
+@@ -472,6 +472,24 @@
+
+ set net_stat = $status
+
++if ("$?NCBI_MT_OTHERLIBS" == "1") then
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ THREAD_OBJ=$NCBI_THREAD_OBJ \
++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++else
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++endif
++eval echo $CMD
++eval echo $CMD | sh
++
+ if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
+ echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
+ cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
new file mode 100644
index 000000000000..cb7d1adf9208
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
@@ -0,0 +1,37 @@
+--- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200
++++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100
+@@ -485,6 +485,34 @@
+
+ set net_stat = $status
+
++if ( $net_stat == 0 ) then
++ # Compile additional tools, usually hidden
++ if ( ! $?EXTRA_VIB ) then
++ set EXTRA_VIB = ( asn2all )
++ endif
++
++ if ("$?NCBI_MT_OTHERLIBS" == "1") then
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ THREAD_OBJ=$NCBI_THREAD_OBJ \
++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
++ else
++ set CMD='make $MFLG -f makenet.unx \
++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
++ endif
++ eval echo $CMD
++ eval echo $CMD | sh
++
++ set net_stat = $status
++
++endif
++
+ if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
+ echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
+ cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
new file mode 100644
index 000000000000..867b203aecb1
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
@@ -0,0 +1,15 @@
+--- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500
++++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500
+@@ -9,10 +9,10 @@
+ #it appears the flags above do not work anymore with newer libc,
+ #the new flags should work. Dima. 08/23/01
+ NCBI_AR=ar
+-NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
++NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+ NCBI_CFLAGS1 = -c
+ NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES
+-NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE
++NCBI_OPTFLAG = -O3 -D_LARGE_FILE
+ NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin
+ NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin
+ NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc
new file mode 100644
index 000000000000..dd77b452fe74
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbirc
@@ -0,0 +1,2 @@
+[NCBI]
+Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/ncbi-tools/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
new file mode 100644
index 000000000000..5542dd5f67b2
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic prefix toolchain-funcs
+
+DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc static-libs X"
+
+RDEPEND="
+ app-shells/tcsh
+ dev-lang/perl
+ media-libs/libpng:0=
+ X? (
+ media-libs/fontconfig
+ x11-libs/motif:0=
+ x11-libs/libICE
+ x11-libs/libX11
+ x11-libs/libXft
+ x11-libs/libXmu
+ x11-libs/libXt
+ )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/ncbi"
+
+EXTRA_VIB="asn2all asn2asn"
+
+pkg_setup() {
+ echo
+ ewarn 'Please note that the NCBI toolkit (and especially the X'
+ ewarn 'applications) are known to have compilation and run-time'
+ ewarn 'problems when compiled with agressive compilation flags. The'
+ ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
+ ewarn 'X support is enabled.'
+ echo
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${PN}-extra_vib.patch \
+ "${FILESDIR}"/${P}-bfr-overflow.patch \
+ "${FILESDIR}"/${P}-format-security.patch \
+ "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch
+
+ if use ppc || use ppc64; then
+ epatch "${FILESDIR}"/${PN}-lop.patch
+ fi
+
+ if ! use X; then
+ sed \
+ -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
+ -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
+ -i "${S}"/make/makedis.csh || die
+ else
+ # X applications segfault on startup on x86 with -O3.
+ use x86 || replace-flags '-O3' '-O2'
+ fi
+
+ # Apply user C flags...
+ cd "${S}"/platform
+ sed \
+ -e "s:-O[s0-9]\?::g" \
+ -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
+ -e 's:-x[A-Z]*::g' \
+ -e 's:-pipe::g' \
+ -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
+ -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
+ -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
+ -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
+ -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
+ -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
+ -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
+ -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
+ -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
+ -i * || die
+
+ # We use dynamic libraries
+ sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
+
+ sed \
+ -re "s:/usr(/bin/.*sh):\1:g" \
+ -e "s:(/bin/.*sh):${EPREFIX}\1:g" \
+ -i $(find "${S}" -type f) || die
+}
+
+src_compile() {
+ export EXTRA_VIB
+ cd "${WORKDIR}"
+ csh ncbi/make/makedis.csh || die
+ mkdir "${S}"/cgi "${S}"/real || die
+ mv "${S}"/bin/*.cgi "${S}"/cgi || die
+ mv "${S}"/bin/*.REAL "${S}"/real || die
+ cd "${S}"/demo
+ emake \
+ -f ../make/makenet.unx \
+ CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \
+ LDFLAGS="${LDFLAGS}" \
+ spidey
+ cp spidey ../bin/ || die
+}
+
+src_install() {
+ #sci-geosciences/cdat-lite
+ mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
+
+ dobin "${S}"/bin/*
+
+ for i in ${EXTRA_VIB}; do
+ dobin "${S}"/build/${i} || die "Failed to install binaries."
+ done
+ use static-libs && dolib.a "${S}"/lib/*.a
+ mkdir -p "${ED}"/usr/include/ncbi
+ cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
+ die "Failed to install headers."
+
+ # TODO: wwwblast with webapps
+ #insinto /usr/share/ncbi/lib/cgi
+ #doins ${S}/cgi/*
+ #insinto /usr/share/ncbi/lib/real
+ #doins ${S}/real/*
+
+ # Basic documentation
+ dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}}
+ newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
+ newdoc "${S}"/config/README README.config
+ newdoc "${S}"/network/encrypt/README README.encrypt
+ newdoc "${S}"/network/nsclilib/readme README.nsclilib
+ newdoc "${S}"/sequin/README README.sequin
+ mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
+ doman "${S}"/doc/man/*
+
+ # Hypertext user documentation
+ dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
+ insinto /usr/share/doc/${PF}/html
+ doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
+
+ # Developer documentation
+ if use doc; then
+ # Demo programs
+ mkdir "${ED}"/usr/share/ncbi
+ mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
+ fi
+
+ # Shared data (similarity matrices and such) and database directory.
+ insinto /usr/share/ncbi
+ doins -r "${S}"/data
+ dodir /usr/share/ncbi/formatdb
+
+ # Default config file to set the path for shared data.
+ insinto /etc/ncbi
+ newins "${FILESDIR}"/ncbirc .ncbirc
+ eprefixify "${ED}"/etc/ncbi/.ncbirc
+
+ # Env file to set the location of the config file and BLAST databases.
+ newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
+}
diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest
new file mode 100644
index 000000000000..fa2d5255b412
--- /dev/null
+++ b/sci-biology/newick-utils/Manifest
@@ -0,0 +1,2 @@
+DIST newick-utils-1.3.0.tar.gz 6872730 SHA256 2c4d364a6b74d484b795681a08f648e1c89c373e6aa29c2b84bf690530bc54ee
+DIST newick-utils-1.5.0.tar.gz 7400423 SHA256 b5508ff31228c8d9fc9fb2e9b70aa24192248998c4e315dd82135323c05e1f67
diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/newick-utils/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/newick-utils/newick-utils-1.3.0.ebuild b/sci-biology/newick-utils/newick-utils-1.3.0.ebuild
new file mode 100644
index 000000000000..94c51c218310
--- /dev/null
+++ b/sci-biology/newick-utils/newick-utils-1.3.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)"
+HOMEPAGE="http://cegg.unige.ch/newick_utils"
+SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="!dev-games/libnw"
+
+src_install() {
+ einstall || die
+}
+
+src_test() {
+ emake -C tests check-TESTS || die
+}
diff --git a/sci-biology/newick-utils/newick-utils-1.5.0.ebuild b/sci-biology/newick-utils/newick-utils-1.5.0.ebuild
new file mode 100644
index 000000000000..6bf8d108ca81
--- /dev/null
+++ b/sci-biology/newick-utils/newick-utils-1.5.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)"
+HOMEPAGE="http://cegg.unige.ch/newick_utils"
+SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="!dev-games/libnw"
+
+src_install() {
+ einstall || die
+}
+
+src_test() {
+ emake -C tests check-TESTS || die
+}
diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
new file mode 100644
index 000000000000..17c26994a8c4
--- /dev/null
+++ b/sci-biology/njplot/Manifest
@@ -0,0 +1 @@
+DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca
diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
new file mode 100644
index 000000000000..61f8b95ea160
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
@@ -0,0 +1,59 @@
+ makefile | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/makefile b/makefile
+index ccb7dc2..9488c2a 100644
+--- a/makefile
++++ b/makefile
+@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF
+ #PDFLIB = -L$(PDF) -lpdf
+
+ # c compiler and linker
+-CC = gcc
++CC ?= gcc
+
+ # Vibrant top directory
+-VIBRANT = /banques0/ncbiJun04
++VIBRANT = /usr/include/ncbi
+
+
+ # X11 include directory
+@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o
+ OBJUNROOTED = unrooted-vib.o preptree.o
+
+
+-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
++CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
+ -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \
+- -Wimplicit-function-declaration -g
++ -Wimplicit-function-declaration
+
+ all: njplot unrooted newicktops newicktotxt
+
+
+ njplot : $(OBJECTS)
+- $(CC) -g -o njplot $(OBJECTS) \
++ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \
+ -L$(VIBRANT)/lib \
+ -lvibrant -lncbi \
+ $(PDFLIB) \
+@@ -40,16 +40,16 @@ njplot : $(OBJECTS)
+ -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
+
+ unrooted : $(OBJUNROOTED)
+- $(CC) -g -o unrooted $(OBJUNROOTED) \
++ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \
+ -L$(VIBRANT)/lib -lvibrant -lncbi \
+ -L$(MOTIFLIB) -lXm \
+ -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
+
+ newicktops: njplot-vib.c
+- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm
++ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm
+
+ newicktotxt: njplot-vib.c
+- $(CC) -DTTY -o $@ njplot-vib.c -lm
++ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm
+
+
+ .c.o :
diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch
new file mode 100644
index 000000000000..686b8475e9ed
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch
@@ -0,0 +1,16 @@
+ njplot-vib.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/njplot-vib.c b/njplot-vib.c
+index fe55609..63fd3b6 100644
+--- a/njplot-vib.c
++++ b/njplot-vib.c
+@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n"
+ #else
+ fprintf(stderr,
+ #endif
+- message);
++ "%s", message);
+ exit(0);
+ }
+ }
diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml
new file mode 100644
index 000000000000..31592430880f
--- /dev/null
+++ b/sci-biology/njplot/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ NJplot is a tree drawing program able to draw any phylogenetic tree
+ expressed in the Newick phylogenetic tree format (e.g., the format used
+ by the PHYLIP package). NJplot is especially convenient for rooting the
+ unrooted trees obtained from parsimony, distance or maximum likelihood
+ tree-building methods.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/njplot/njplot-2.3-r1.ebuild b/sci-biology/njplot/njplot-2.3-r1.ebuild
new file mode 100644
index 000000000000..f766af55ea96
--- /dev/null
+++ b/sci-biology/njplot/njplot-2.3-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+ sci-biology/ncbi-tools[X,static-libs]
+ x11-libs/libXmu"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ sed -i -e "s%njplot.help%${EPREFIX}/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die
+ epatch \
+ "${FILESDIR}"/${P}-format-security.patch \
+ "${FILESDIR}"/${P}-buildsystem.patch
+ tc-export CC
+}
+
+src_install() {
+ dobin newicktops newicktotxt njplot unrooted
+ doman *.1
+ dodoc README njplot.help
+}
diff --git a/sci-biology/njplot/njplot-2.3.ebuild b/sci-biology/njplot/njplot-2.3.ebuild
new file mode 100644
index 000000000000..03bcad009906
--- /dev/null
+++ b/sci-biology/njplot/njplot-2.3.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit toolchain-funcs
+
+DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND="
+ sci-biology/ncbi-tools[X,static-libs]
+ x11-libs/libXmu"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ sed -i -e 's|/banques0/ncbiJun04|/usr/include/ncbi|' \
+ -e 's/CC = gcc/CC='$(tc-getCC)'/' -e 's/CFLAGS =/CFLAGS +=/' \
+ makefile || die
+ sed -i -e "s%njplot.help%/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die
+}
+
+src_install() {
+ dobin newicktops newicktotxt njplot unrooted || die
+ doman *.1 || die
+ dodoc README njplot.help
+}
diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest
new file mode 100644
index 000000000000..b024eadc948a
--- /dev/null
+++ b/sci-biology/pals/Manifest
@@ -0,0 +1 @@
+DIST pals-1.0.tar.gz 24895 SHA256 2768adfdd93f56f859744ff9bbbabcc4571b38fa8ea247d505599beee3a962c2
diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/pals/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/pals/pals-1.0.ebuild b/sci-biology/pals/pals-1.0.ebuild
new file mode 100644
index 000000000000..283bf5d6dfca
--- /dev/null
+++ b/sci-biology/pals/pals-1.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit toolchain-funcs
+
+DESCRIPTION="Pairwise Aligner for Long Sequences"
+HOMEPAGE="http://www.drive5.com/pals/"
+#SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_compile() {
+ emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
+}
+
+src_install() {
+ dobin pals || die
+}
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
new file mode 100644
index 000000000000..f4ddf21f97d9
--- /dev/null
+++ b/sci-biology/paml/Manifest
@@ -0,0 +1 @@
+DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/paml/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
new file mode 100644
index 000000000000..7868859871b9
--- /dev/null
+++ b/sci-biology/paml/paml-4.4c-r1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs versionator
+
+MY_P=$(version_format_string '${PN}$1$2')
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+ # Notice send by mail to prof. Ziheng Yang
+ sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
+}
+
+src_compile() {
+ emake -C src \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS} -Wno-unused-result" \
+ LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ dodoc README.txt doc/*
+
+ insinto /usr/share/${PN}/control
+ doins *.ctl
+
+ insinto /usr/share/${PN}/dat
+ doins stewart* *.dat dat/*
+
+ insinto /usr/share/${PN}
+ doins -r examples/
+
+ cd src || die
+ dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+}
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
new file mode 100644
index 000000000000..1275fda8b314
--- /dev/null
+++ b/sci-biology/phrap/Manifest
@@ -0,0 +1 @@
+DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/phrap/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/phrap/phrap-1.080812-r1.ebuild b/sci-biology/phrap/phrap-1.080812-r1.ebuild
new file mode 100644
index 000000000000..d6864dc373cb
--- /dev/null
+++ b/sci-biology/phrap/phrap-1.080812-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Shotgun assembly and alignment utilities"
+HOMEPAGE="http://www.phrap.org/"
+SRC_URI="phrap-${PV}-distrib.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+ dev-lang/perl
+ dev-perl/perl-tk"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
+ einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\""
+ einfo "and put it in ${DISTDIR}"
+}
+
+src_prepare() {
+ sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die
+ sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die
+}
+
+src_install() {
+ dobin cross_match loco phrap phrapview swat
+ newbin cluster cluster_phrap
+ for i in {general,phrap,swat}.doc ; do
+ newdoc ${i} ${i}.txt
+ done
+}
diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
new file mode 100644
index 000000000000..92cfe6ce81b8
--- /dev/null
+++ b/sci-biology/phred/Manifest
@@ -0,0 +1 @@
+DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975
diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/phred/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/phred/phred-071220.ebuild b/sci-biology/phred/phred-071220.ebuild
new file mode 100644
index 000000000000..22600ba92c50
--- /dev/null
+++ b/sci-biology/phred/phred-071220.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A base caller for Sanger DNA sequencing"
+HOMEPAGE="http://phrap.org/phredphrapconsed.html"
+SRC_URI="phred-dist-071220.b-acd.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ elog "Please visit ${HOMEPAGE} and obtain the file"
+ elog "${SRC_URI}, then place it in ${DISTDIR}"
+}
+
+src_compile() {
+ sed -i -e 's/CFLAGS=/CFLAGS += /' Makefile
+ emake daev || die
+ emake || die
+}
+
+src_install() {
+ dobin phred daev || die
+ insinto /usr/share/${PN}
+ doins phredpar.dat || die
+ echo "PHRED_PARAMETER_FILE=/usr/share/${PN}/phredpar.dat" > 99phred
+ doenvd 99phred || die
+ newdoc DAEV.DOC DAEV.DOC.txt
+ newdoc PHRED.DOC PHRED.DOC.txt
+}
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
new file mode 100644
index 000000000000..5971f2782bbb
--- /dev/null
+++ b/sci-biology/phylip/Manifest
@@ -0,0 +1,2 @@
+DIST phylip-3.69.tar.gz 1511935 SHA256 27947ce8dab4416e4823db38b3d1b0bf17bc545b6907cf09dcf6177df94c1a8f SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d WHIRLPOOL 25c45ac2a96278eaef9a62aecc367aa32a894df0cd5aff9b626abd013ecbe52f9d4bdaf7805ba5c5d8699f9a74d3d26cfe6e1c1b22960c03061171625d16415f
+DIST phylip-3.696.tar.gz 3955721 SHA256 cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be WHIRLPOOL 7d4d4bd703ecd84b7570c937484c15f52643221ca178fb494f81b18991149fc2f8d1c8c5b99b57e20ada0bef7e93dcb15c55410f8f1012b1656419fab19b3cab
diff --git a/sci-biology/phylip/files/README.Gentoo b/sci-biology/phylip/files/README.Gentoo
new file mode 100644
index 000000000000..3b2062003996
--- /dev/null
+++ b/sci-biology/phylip/files/README.Gentoo
@@ -0,0 +1,15 @@
+Using the PHYlogeny Inference Package on Gentoo systems
+
+Location of the factor program
+
+On Gentoo systems, the PHYLIP program "factor" is named "factor-phylip", in
+order to avoid a file collision with the program of the same name provided by
+the "sys-apps/coreutils" package.
+
+Location of the font files
+
+PHYLIP programs will find font files only if they are in a directory
+referenced by the "PATH" variable or if they are in the current working
+directory. When working with PHYLIP programs that need these files, either
+copy or symlink the fonts you need to your working directory, or add
+"/usr/share/phylip/fonts/" to your "PATH" variable.
diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/phylip/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
new file mode 100644
index 000000000000..ecc44200ac57
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.69-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="freedist"
+IUSE=""
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND="x11-libs/libXaw"
+DEPEND="${RDEPEND}
+ x11-proto/xproto"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+ sed \
+ -e "s/CFLAGS = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
+ -e "s/CC = cc/CC = $(tc-getCC)/" \
+ -e "s/DC = cc/DC = $(tc-getCC)/" \
+ -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
+ -i Makefile || die "Patching Makefile failed."
+ mkdir ../fonts || die
+}
+
+src_compile() {
+ emake -j1 all put
+}
+
+src_install() {
+ cd "${WORKDIR}/${P}" || die
+
+ mv exe/font* fonts || die "Font move failed."
+ mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
+
+ dobin exe/*
+
+ dodoc "${FILESDIR}"/README.Gentoo
+
+ dohtml -r phylip.html doc
+
+ insinto /usr/share/${PN}/
+ doins -r fonts
+}
diff --git a/sci-biology/phylip/phylip-3.696.ebuild b/sci-biology/phylip/phylip-3.696.ebuild
new file mode 100644
index 000000000000..d5960bb62bb7
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.696.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND="x11-libs/libXaw"
+DEPEND="${RDEPEND}
+ x11-proto/xproto"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+ mv Makefile.unx Makefile || die
+ sed \
+ -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
+ -i Makefile || die "Patching Makefile failed."
+ mkdir ../fonts || die
+}
+
+src_compile() {
+ emake -j1 \
+ CC="$(tc-getCC)" \
+ DC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS} -Wno-unused-result" \
+ all put
+}
+
+src_install() {
+ cd "${WORKDIR}/${P}" || die
+
+ mv exe/font* fonts || die "Font move failed."
+ mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
+
+ dobin exe/*
+
+ dodoc "${FILESDIR}"/README.Gentoo
+
+ dohtml -r phylip.html doc
+
+ insinto /usr/share/${PN}/
+ doins -r fonts
+}
diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest
new file mode 100644
index 000000000000..d285799277e1
--- /dev/null
+++ b/sci-biology/phyml/Manifest
@@ -0,0 +1 @@
+DIST phyml_v2.4.5.tar.gz 92143 SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3 WHIRLPOOL e9c0e36ea871c61fc617ed0a10d306bdb66d84da0b9a08107fb9e1f6370e10676c5ad8a0a5e5404ccad6ae2f62551d566614a173cfdd4a0a523f727fc7924ce0
diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml
new file mode 100644
index 000000000000..d0355f85e406
--- /dev/null
+++ b/sci-biology/phyml/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription lang="en">
+ Phyml is a simple, fast, and accurate algorithm to estimate large
+ phylogenies by maximum likelihood. Given input sequence files, it
+ estimates phylogenies using maximum likelihood, and is capable of
+ processing large amounts of phylogenetic data.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/phyml/phyml-2.4.5-r2.ebuild b/sci-biology/phyml/phyml-2.4.5-r2.ebuild
new file mode 100644
index 000000000000..7d9815baa78b
--- /dev/null
+++ b/sci-biology/phyml/phyml-2.4.5-r2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+inherit toolchain-funcs
+
+MY_P=${PN}_v${PV}
+
+DESCRIPTION="Estimation of large phylogenies by maximum likelihood"
+HOMEPAGE="http://atgc.lirmm.fr/phyml/"
+SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+ sed -e 's/^hello !!!//' \
+ -e 's/$(CC) -o/$(CC) $(LDFLAGS) -o/' \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake -e CC="$(tc-getCC)" || die
+}
+
+src_install() {
+ dobin phyml || die
+}
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
new file mode 100644
index 000000000000..814765877966
--- /dev/null
+++ b/sci-biology/picard/Manifest
@@ -0,0 +1 @@
+DIST picard-1.103.tar.bz2 15037887 SHA256 777af2a0aadd97a2b909160774e6e0ad99cef6de7763096f10660ccbe2baca63 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca WHIRLPOOL de5a0341473174bfc7a1f1b8d1b3b6122b212a1d964dda534912347595a3da9fe2a86692959df7375896292e3f3657a9c27c2f1694fca60d48ff23192b93b098
diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch
new file mode 100644
index 000000000000..00e89b95056a
--- /dev/null
+++ b/sci-biology/picard/files/1.103-gentoo.patch
@@ -0,0 +1,131 @@
+diff --git a/build.xml b/build.xml
+index fca2271..11f4fbd 100755
+--- a/build.xml
++++ b/build.xml
+@@ -52,9 +52,6 @@
+ <property name="testng.verbosity" value="2"/>
+ <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
+
+- <property environment="env"/>
+- <property name="java6.home" value="${env.JAVA6_HOME}"/>
+-
+ <condition property="isUnix">
+ <os family="unix"/>
+ </condition>
+@@ -78,9 +75,6 @@
+ <pathelement location="${classes}"/>
+ </path>
+
+- <path id="java6.lib.ref">
+- <fileset dir="${java6.home}/lib" includes="*.jar"/>
+- </path>
+ </target>
+
+ <!-- CLEAN -->
+@@ -94,10 +88,6 @@
+ </target>
+
+ <!-- COMPILE -->
+- <target name="compile" depends="compile-src, compile-tests"
+- description="Compile files without cleaning">
+- </target>
+-
+ <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/>
+
+ <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning">
+@@ -138,7 +128,7 @@
+ </target>
+
+ <!-- TEST -->
+- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests">
++ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests">
+ <taskdef resource="testngtasks" classpathref="classpath"/>
+ <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}"
+ failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}"
+@@ -151,6 +141,8 @@
+ <classfileset dir="${classes.test}">
+ <include name="**/Test*.class"/>
+ <include name="**/*Test.class"/>
++ <exclude name="**/ValidateSamFileTest.class" />
++ <exclude name="**/VCFWriterUnitTest.class" />
+ </classfileset>
+ <jvmarg value="-Xmx2G"/>
+ </testng>
+@@ -165,7 +157,7 @@
+ </target>
+
+ <target name="single-test"
+- depends="compile, compile-tests"
++ depends="compile-tests"
+ description="Compile and run a single test.">
+ <taskdef resource="testngtasks" classpathref="classpath"/>
+ <fail unless="name" message="Please provide input test: -Dname=..." />
+@@ -200,13 +192,12 @@
+ </jar>
+ </target>
+
+- <target name="picard-jar" depends="compile"
++ <target name="picard-jar" depends="compile-src"
+ description="Builds picard-${picard-version}.jar for inclusion in other projects">
+ <mkdir dir="${dist}"/>
+ <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
+ <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
+ <fileset dir="${src.scripts}" includes="**/*.R"/>
+- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
+ <manifest>
+ <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
+ <attribute name="Implementation-Vendor" value="Broad Institute"/>
+@@ -214,7 +205,7 @@
+ </jar>
+ </target>
+
+- <target name="tribble-jar" depends="compile"
++ <target name="tribble-jar" depends="compile-src"
+ description="Builds tribble-${tribble-version}.jar for inclusion in other projects">
+ <mkdir dir="${dist}"/>
+ <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no">
+@@ -225,7 +216,7 @@
+ </copy>
+ </target>
+
+- <target name="variant-jar" depends="compile"
++ <target name="variant-jar" depends="compile-src"
+ description="Builds variant-${variant-version}.jar for inclusion in other projects">
+ <mkdir dir="${dist}"/>
+ <jar destfile="${dist}/variant-${variant-version}.jar" compress="no">
+@@ -262,7 +253,7 @@
+ </javadoc>
+ </target>
+
+- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar">
++ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar">
+ <delete dir="${command_tmp}"/>
+
+ <mkdir dir="${command_tmp}"/>
+@@ -344,7 +335,7 @@
+ </target>
+
+ <!-- ALL -->
+- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
++ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
+ <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
+ <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
+ <zipfileset dir="${lib}" includes="snappy*.jar"/>
+@@ -468,8 +459,6 @@
+ target="${javac.target}">
+ <classpath refid="@{compile.classpath}"/>
+ <compilerarg line="@{compiler.args}" />
+- <!-- ensure that Java 6 bootclasspath is used -->
+- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
+ </javac>
+ </sequential>
+ </macrodef>
+@@ -494,8 +483,6 @@
+ <pathelement location="${classes}"/>
+ </classpath>
+ <compilerarg line="@{compiler.args}"/>
+- <!-- ensure that Java 6 bootclasspath is used -->
+- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
+ </javac>
+ </sequential>
+ </macrodef>
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
new file mode 100644
index 000000000000..265affea91d0
--- /dev/null
+++ b/sci-biology/picard/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>ercpe@gentoo.org</email>
+ <name>Johann Schmitz (ercpe)</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild
new file mode 100644
index 000000000000..16e71f41f2b0
--- /dev/null
+++ b/sci-biology/picard/picard-1.103.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+JAVA_PKG_IUSE="doc source test"
+WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
+HOMEPAGE="http://picard.sourceforge.net/"
+SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/snappy:1.0
+ dev-java/cofoja:0
+ dev-java/commons-jexl:2
+ dev-java/ant-core:0"
+
+DEPEND=">=virtual/jdk-1.6
+ dev-java/ant-apache-bcel:0
+ test? (
+ dev-java/testng:0
+ dev-lang/R
+ )
+ ${CDEPEND}"
+RDEPEND=">=virtual/jre-1.6
+ ${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_TEST_TARGET="test"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
+EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
+
+java_prepare() {
+ mkdir "${S}"/lib || die
+
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+
+ mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
+}
+
+src_install() {
+ cd dist || die
+
+ for i in *-${PV}.jar; do
+ java-pkg_newjar $i ${i/-${PV}/}
+ rm $i || die
+ done
+
+ java-pkg_dojar *.jar
+ for i in *.jar; do
+ java-pkg_dolauncher ${i/.jar/} --jar $i;
+ done
+
+ use source && java-pkg_dosrc "${S}"/src/java/*
+ use doc && java-pkg_dojavadoc "${S}"/javadoc
+}
+
+src_test() {
+ java-pkg-2_src_test
+}
diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest
new file mode 100644
index 000000000000..a63f193ecb5b
--- /dev/null
+++ b/sci-biology/piler/Manifest
@@ -0,0 +1 @@
+DIST piler-1.0.tar.gz 35220 SHA256 2940530c0afd7e49ca6e9cd8a1e3fd9890d87c71f9c19a42b1e468add83ccc69
diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
new file mode 100644
index 000000000000..4c7f124c5e3d
--- /dev/null
+++ b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
@@ -0,0 +1,12 @@
+diff -ur piler.orig/gff.cpp piler/gff.cpp
+--- piler.orig/gff.cpp 2004-12-18 01:25:29.000000000 +0200
++++ piler/gff.cpp 2009-08-09 17:22:33.000000000 +0300
+@@ -70,7 +70,7 @@
+ const char *Attrs = Fields[8];
+
+ // Truncate attrs if comment found
+- char *Pound = strchr(Attrs, '#');
++ char *Pound = const_cast <char*> (strchr(Attrs, '#'));
+ if (0 != Pound)
+ *Pound = 0;
+
diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/piler/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/piler/piler-1.0.ebuild b/sci-biology/piler/piler-1.0.ebuild
new file mode 100644
index 000000000000..139f92cda50f
--- /dev/null
+++ b/sci-biology/piler/piler-1.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Analysis of repetitive DNA found in genome sequences"
+HOMEPAGE="http://www.drive5.com/piler/"
+#SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="|| ( sci-biology/muscle
+ sci-libs/libmuscle )
+ sci-biology/pals"
+
+S=${WORKDIR}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+}
+
+src_compile() {
+ emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
+}
+
+src_install() {
+ dobin piler
+}
diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest
new file mode 100644
index 000000000000..b810410070ad
--- /dev/null
+++ b/sci-biology/pilercr/Manifest
@@ -0,0 +1 @@
+DIST pilercr-1.0.tar.gz 1709144 SHA256 75f58d58567c478e271c4c554071a7d6d642e6daef8981ee2618daa7b53fa923
diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
new file mode 100644
index 000000000000..7b49df872e27
--- /dev/null
+++ b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
@@ -0,0 +1,33 @@
+diff -dur work/multaln.h work-orig/multaln.h
+--- work/multaln.h 2007-04-17 19:02:18.000000000 +0000
++++ work-orig/multaln.h 2009-02-18 21:25:26.166333299 +0000
+@@ -6,6 +6,7 @@
+ #define _CRT_SECURE_NO_DEPRECATE 1
+ #endif
+
++#include <cstring>
+ #include <vector>
+ #include <limits.h>
+ #include <ctype.h>
+diff -dur work/seqvect.h work-orig/seqvect.h
+--- work/seqvect.h 2006-04-06 23:36:18.000000000 +0000
++++ work-orig/seqvect.h 2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef SeqVect_h
+ #define SeqVect_h
+
++#include <stdio.h>
+ #include <vector>
+ #include "seq.h"
+
+diff -dur work/tree.h work-orig/tree.h
+--- work/tree.h 2006-04-05 23:52:42.000000000 +0000
++++ work-orig/tree.h 2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef tree_h
+ #define tree_h
+
++#include <stdlib.h>
+ #include <limits.h>
+
+ class Clust;
diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/pilercr/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/pilercr/pilercr-1.0.ebuild b/sci-biology/pilercr/pilercr-1.0.ebuild
new file mode 100644
index 000000000000..3241d42a863c
--- /dev/null
+++ b/sci-biology/pilercr/pilercr-1.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)"
+HOMEPAGE="http://www.drive5.com/pilercr/"
+#SRC_URI="http://www.drive5.com/pilercr/pilercr.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc43.patch
+}
+
+src_compile() {
+ emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin ${PN}
+}
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
new file mode 100644
index 000000000000..1bd3f237d4c8
--- /dev/null
+++ b/sci-biology/plink/Manifest
@@ -0,0 +1,2 @@
+DIST plink-1.07-src.zip 2257297 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3 WHIRLPOOL 01e69f605e1b52c6087dd75b506a7705d3bdb8e7dfdd0158e125f4fc4d962fad70c4ec430a139029b3b4ae91b822eb10123fab062c6552b946ec96ca7caf37da
+DIST plink-1.90_pre140514.zip 822157 SHA256 c6f93153d079b4b7f9ae4a51a3b4dcc7bc5ed60b408d39fce6234b98570b8ea7 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 WHIRLPOOL ebcccc1dc0461afd973aa63313237bfd5d904543785115fa71f3af1925d8bb21da15bd0baf60e38f4da534c8c554202a7af6c642b274ca9a458fc0035c2758d2
diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch
new file mode 100644
index 000000000000..aa130f29beb2
--- /dev/null
+++ b/sci-biology/plink/files/1.07-flags.patch
@@ -0,0 +1,44 @@
+diff --git a/Makefile b/Makefile
+index 172c795..466f09f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,25 +26,25 @@ WITH_R_PLUGINS = 1
+ WITH_WEBCHECK = 1
+ FORCE_32BIT =
+ WITH_ZLIB = 1
+-WITH_LAPACK =
+-FORCE_DYNAMIC =
++WITH_LAPACK = 1
++FORCE_DYNAMIC = 1
+
+ # Put C++ compiler here; Windows has it's own specific version
+ CXX_UNIX = g++
+ CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
+
+ # Any other compiler flags here ( -Wall, -g, etc)
+-CXXFLAGS =
++CXXFLAGS ?= -O2
+
+ # Misc
+-LIB_LAPACK = /usr/lib/liblapack.so.3
++LIB_LAPACK = `$(PKG_CONFIG) --libs lapack`
+
+
+ # --------------------------------------------------------------------
+ # Do not edit below this line
+ # --------------------------------------------------------------------
+
+-CXXFLAGS += -O3 -I.
++CXXFLAGS += -I.
+ OUTPUT = plink
+
+ # Some system specific flags
+@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o)
+ all : $(OUTPUT)
+
+ $(OUTPUT) :
+- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB)
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB)
+
+ $(OBJ) : $(HDR)
+
diff --git a/sci-biology/plink/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch
new file mode 100644
index 000000000000..6c289edae153
--- /dev/null
+++ b/sci-biology/plink/files/plink-1.07-gcc47.patch
@@ -0,0 +1,64 @@
+ elf.cpp | 6 +++---
+ idhelp.cpp | 8 ++++----
+ sets.cpp | 8 ++++----
+ 3 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/elf.cpp b/elf.cpp
+index ec2ed3d..a57665f 100644
+--- a/elf.cpp
++++ b/elf.cpp
+@@ -1175,10 +1175,10 @@ void Plink::elfBaseline()
+ << setw(8) << gcnt << " "
+ << setw(8) << (double)cnt / (double)gcnt << "\n";
+
+- map<int,int>::iterator i = chr_cnt.begin();
+- while ( i != chr_cnt.end() )
++ map<int,int>::iterator j = chr_cnt.begin();
++ while ( j != chr_cnt.end() )
+ {
+- int c = i->first;
++ int c = j->first;
+ int x = chr_cnt.find( c )->second;
+ int y = chr_gcnt.find( c )->second;
+
+diff --git a/idhelp.cpp b/idhelp.cpp
+index a9244fa..8882097 100644
+--- a/idhelp.cpp
++++ b/idhelp.cpp
+@@ -772,12 +772,12 @@ void IDHelper::idHelp()
+ for (int j = 0 ; j < jointField.size(); j++ )
+ {
+ set<IDField*> & jf = jointField[j];
+- set<IDField*>::iterator j = jf.begin();
++ set<IDField*>::iterator k = jf.begin();
+ PP->printLOG(" { ");
+- while ( j != jf.end() )
++ while ( k != jf.end() )
+ {
+- PP->printLOG( (*j)->name + " " );
+- ++j;
++ PP->printLOG( (*k)->name + " " );
++ ++k;
+ }
+ PP->printLOG(" }");
+ }
+diff --git a/sets.cpp b/sets.cpp
+index 3a8f92f..66787e8 100644
+--- a/sets.cpp
++++ b/sets.cpp
+@@ -768,11 +768,11 @@ vector_t Set::profileTestScore()
+ //////////////////////////////////////////////
+ // Reset original missing status
+
+- vector<Individual*>::iterator i = PP->sample.begin();
+- while ( i != PP->sample.end() )
++ vector<Individual*>::iterator j = PP->sample.begin();
++ while ( j != PP->sample.end() )
+ {
+- (*i)->missing = (*i)->flag;
+- ++i;
++ (*j)->missing = (*j)->flag;
++ ++j;
+ }
+
+ ////////////////////////////////////////////////
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
new file mode 100644
index 000000000000..80af0e1d0365
--- /dev/null
+++ b/sci-biology/plink/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="webcheck">
+ add support for online update checking every time the program starts
+ </flag>
+ <flag name="R">
+ add support R language
+ </flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/plink/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild
new file mode 100644
index 000000000000..ca32ecf62a18
--- /dev/null
+++ b/sci-biology/plink/plink-1.07-r1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Whole genome association analysis toolset"
+HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
+SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="lapack -webcheck R"
+KEYWORDS="amd64 x86"
+
+DEPEND="
+ app-arch/unzip
+ lapack? ( virtual/pkgconfig )"
+RDEPEND="
+ sys-libs/zlib
+ lapack? ( virtual/lapack )"
+
+S="${WORKDIR}/${P}-src"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${PV}-flags.patch \
+ "${FILESDIR}"/${P}-gcc47.patch
+ use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die
+ use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die
+ use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die
+ tc-export PKG_CONFIG
+}
+
+src_compile() {
+ emake \
+ CXX_UNIX=$(tc-getCXX)
+}
+
+src_install() {
+ newbin plink p-link
+ dodoc README.txt
+}
diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild
new file mode 100644
index 000000000000..45b80be23c36
--- /dev/null
+++ b/sci-biology/plink/plink-1.90_pre140514.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Whole genome association analysis toolset"
+HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
+SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ app-arch/unzip
+ virtual/pkgconfig"
+RDEPEND="
+ sys-libs/zlib
+ virtual/cblas
+ virtual/lapack
+ "
+
+S="${WORKDIR}/"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+ sed \
+ -e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
+ -i *.{c,h} || die
+
+ sed \
+ -e 's:g++:$(CXX):g' \
+ -e 's:gcc:$(CC):g' \
+ -e 's:gfortran:$(FC):g' \
+ -i Makefile || die
+ tc-export PKG_CONFIG
+}
+
+src_compile() {
+ emake \
+ CXX=$(tc-getCXX) \
+ CFLAGS="${CFLAGS}" \
+ ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
+ BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
+}
+
+src_install() {
+ newbin plink p-link
+}
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
new file mode 100644
index 000000000000..5a988dfac24d
--- /dev/null
+++ b/sci-biology/poa/Manifest
@@ -0,0 +1 @@
+DIST poaV2.tar.gz 62612 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2
diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch
new file mode 100644
index 000000000000..bdd638cf64b7
--- /dev/null
+++ b/sci-biology/poa/files/2-respect-flags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index a65bed0..713a7ab 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,9 +26,10 @@ LIBOBJECTS= \
+ stringptr.o
+
+
+-CC = gcc
++CC ?= gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+
+@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS)
+
+ # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
+ poa: $(OBJECTS) liblpo.a
+- $(CC) -o $@ $(OBJECTS) -lm liblpo.a
++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
+
+ what:
+ @echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch
new file mode 100644
index 000000000000..2ae08db4ff4d
--- /dev/null
+++ b/sci-biology/poa/files/respect-cflags.patch
@@ -0,0 +1,13 @@
+diff -urN poaV2.orig/Makefile poaV2/Makefile
+--- poaV2.orig/Makefile 2004-03-11 21:33:30.000000000 -0800
++++ poaV2/Makefile 2006-03-09 20:09:27.000000000 -0800
+@@ -28,7 +28,8 @@
+
+ CC = gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
new file mode 100644
index 000000000000..65027f64ec24
--- /dev/null
+++ b/sci-biology/poa/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">poamsa</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
new file mode 100644
index 000000000000..8a1a23ca4902
--- /dev/null
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+MY_P="${PN}V${PV}"
+
+DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
+HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
+SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+
+# According to SF project page
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="static-libs"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-respect-flags.patch
+}
+
+src_compile() {
+ emake \
+ CC="$(tc-getCC)" \
+ OPT_CFLAGS="${CFLAGS}" \
+ poa
+}
+
+src_install() {
+ dobin "${S}"/poa "${S}"/make_pscores.pl
+ use static-libs && dolib.a "${S}"/liblpo.a
+ dodoc "${S}"/README "${S}"/multidom.*
+ insinto /usr/share/poa
+ doins "${S}"/*.mat
+}
+
+pkg_postinst() {
+ elog "poa requires a score matrix as the first argument."
+ elog "This package installs two examples to ${EROOT}usr/share/poa/."
+}
diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest
new file mode 100644
index 000000000000..96826545f7c3
--- /dev/null
+++ b/sci-biology/prank/Manifest
@@ -0,0 +1,3 @@
+DIST prank.source.140603.tgz 150346 SHA256 9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 WHIRLPOOL 5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6
+DIST prank.src.100701.tgz 115444 SHA256 2ba63fc8f998a86e6fc688170b03f831eeb8d8deda95cbf0986e8a3a3b09ec79
+DIST prank.src.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c WHIRLPOOL 37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b
diff --git a/sci-biology/prank/files/prank-111130-gcc-4.7.patch b/sci-biology/prank/files/prank-111130-gcc-4.7.patch
new file mode 100644
index 000000000000..d7defbcadfec
--- /dev/null
+++ b/sci-biology/prank/files/prank-111130-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/check_version.cpp | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/check_version.cpp b/src/check_version.cpp
+index e968a05..6dfa062 100644
+--- a/src/check_version.cpp
++++ b/src/check_version.cpp
+@@ -8,6 +8,7 @@
+ #include <string>
+ #include <sstream>
+ #include <iostream>
++#include <unistd.h>
+
+ using namespace std;
+
diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml
new file mode 100644
index 000000000000..2cd3c04eeca0
--- /dev/null
+++ b/sci-biology/prank/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="google-code">prank-msa</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/prank/prank-100701.ebuild b/sci-biology/prank/prank-100701.ebuild
new file mode 100644
index 000000000000..913ff56ee71b
--- /dev/null
+++ b/sci-biology/prank/prank-100701.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S=${WORKDIR}/${PN}
+
+src_prepare() {
+ sed -i -e "s/\$(LINK)/& \$(LDFLAGS)/" Makefile || die
+}
+
+src_compile() {
+ emake \
+ LINK="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ CFLAGS="${CFLAGS}" \
+ CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin prank
+}
diff --git a/sci-biology/prank/prank-111130.ebuild b/sci-biology/prank/prank-111130.ebuild
new file mode 100644
index 000000000000..4d4f6e912495
--- /dev/null
+++ b/sci-biology/prank/prank-111130.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://prank-msa.googlecode.com/files/prank.src.${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/prank-msa/src"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc-4.7.patch
+ sed \
+ -e "s/\$(LINK)/& \$(LDFLAGS)/" \
+ -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake \
+ LINK="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ CFLAGS="${CFLAGS}" \
+ CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin prank
+}
diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild
new file mode 100644
index 000000000000..a18b7ab9d553
--- /dev/null
+++ b/sci-biology/prank/prank-140603.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${PN}-msa/src"
+
+src_prepare() {
+ sed \
+ -e "s/\$(LINK)/& \$(LDFLAGS)/" \
+ -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake \
+ LINK="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ CFLAGS="${CFLAGS}" \
+ CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin ${PN}
+}
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
new file mode 100644
index 000000000000..19da14fe3f93
--- /dev/null
+++ b/sci-biology/primer3/Manifest
@@ -0,0 +1,2 @@
+DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666
+DIST primer3-src-2.3.6.tar.gz 1667573 SHA256 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead WHIRLPOOL 61bbc676c38b1b96806c9ac54d130aae936a5406213759613a3be76016cdd4ebf76c5a54d1ceffc7bd2634829d9aef9d64f87cc85289793b40ab031e01a5917f
diff --git a/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch
new file mode 100644
index 000000000000..66a5a52d4e8e
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch
@@ -0,0 +1,25 @@
+Respect LDFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=335225
+
+--- src/Makefile
++++ src/Makefile
+@@ -103,10 +103,10 @@
+ $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+ oligotm: oligotm_main.c oligotm.h $(OLIGOTM_LIB)
+- $(CC) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
+
+ long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
+- $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+ boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c
+@@ -136,4 +136,4 @@
+ primer_test: test
+
+ test: $(PRIMER_EXE) ntdpal
+- cd ../test; make test
++ $(MAKE) -C ../test test
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
new file mode 100644
index 000000000000..cf47b35af502
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
@@ -0,0 +1,148 @@
+ src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
+ 1 file changed, 31 insertions(+), 30 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index 607ab45..a88adf4 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -52,15 +52,16 @@ TESTOPTS=
+ WINMAKE=mingw32-make
+
+ LDLIBS = -lm
+-AR = ar
+-CC = gcc
+-CPP = g++
+-O_OPTS = -O2
+-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__
+-P_DEFINES =
++AR ?= ar
++CC ?= gcc
++CXX ?= g++
++O_OPTS ?=
++CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__
++P_DEFINES ?=
+
+-CFLAGS = $(CC_OPTS) $(O_OPTS)
+-LDFLAGS = -g
++CFLAGS += $(CC_OPTS) $(O_OPTS)
++CXXFLAGS += $(CC_OPTS) $(O_OPTS)
++LDFLAGS +=
+ # Note, for profiling, use
+ # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
+
+@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a
+ LIBPRIMER3_DYN = libprimer3.so.1.0.0
+ LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM)
+ DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
+-RANLIB = ranlib
++RANLIB ?= ranlib
+
+ PRIMER_OBJECTS1=primer3_boulder_main.o\
+ format_output.o\
+@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
+ $(RANLIB) $@
+
+ $(LIBOLIGOTM_LIB): oligotm.o
+- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
++ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
+
+ $(LIBDPAL): dpal_primer.o
+ $(AR) rv $@ dpal_primer.o
+ $(RANLIB) $@
+
+ $(LIBDPAL_DYN): dpal_primer.o
+- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
++ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
+
+ $(LIBTHAL): thal_primer.o
+ $(AR) rv $@ thal_primer.o
+ $(RANLIB) $@
+
+ $(LIBTHAL_DYN): thal_primer.o
+- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
++ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
+
+ $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
+ $(AR) rv $@ libprimer3.o p3_seq_lib.o
+ $(RANLIB) $@
+
+ $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
+- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
++ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
+
+ $(PRIMER_EXE): $(PRIMER_OBJECTS)
+- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
++ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+
+ libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
+- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
++ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
+
+ $(NTDPAL_EXE): ntdpal_main.o dpal.o
+- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
++ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+ $(NTTHAL_EXE): thal_main.o thal.o
+- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
++ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
+
+ $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
+- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
+
+ $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
+- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+ read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h
+- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
+
+ print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
+- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
+
+ dpal.o: dpal.c dpal.h
+- $(CPP) -c $(CFLAGS) -o $@ dpal.c
++ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c
+
+ # We use '-ffloat-store' on windows to prevent undesirable
+ # precision which may lead to differences in floating point results.
+ thal.o: thal.c thal.h
+- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
++ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
+
+ p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
+- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
++ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
+
+ dpal_primer.o: dpal.c dpal.h
+- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
+
+ thal_primer.o: thal.c thal.h
+- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
++ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
+
+ format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
+- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
+
+ ntdpal_main.o: ntdpal_main.c dpal.h
+- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
++ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
+
+ thal_main.o: thal_main.c thal.h
+- $(CPP) -c $(CFLAGS) -o $@ thal_main.c
++ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
+ # We use CC_OPTS above rather than CFLAGS because
+ # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
+
+ oligotm.o: oligotm.c oligotm.h
+
+ primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
+- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
+
+ primer_test: test
+
diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml
new file mode 100644
index 000000000000..1fbadfaf3b77
--- /dev/null
+++ b/sci-biology/primer3/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ Primer3 picks primers for PCR reactions, considering: oligonucleotide
+ melting temperature, size, GC content, and primer-dimer possibilities;
+ PCR product size; positional constraints within the source sequence;
+ and miscellaneous other constraints. All of these criteria are
+ user-specifiable as constraints, and some are specifiable as terms in
+ an objective function that characterizes an optimal primer pair.
+ </longdescription>
+ <upstream>
+ <remote-id type="sourceforge">primer3</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild
new file mode 100644
index 000000000000..4135610c2524
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.5.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+ if [[ ${CHOST} == *-darwin* ]]; then
+ sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+ fi
+
+ tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+ emake -C src
+}
+
+src_test () {
+ emake -C test | tee "${T}"/test.log
+ grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+ dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+ dodoc src/release_notes.txt example
+ insinto /opt/primer3_config
+ doins -r src/primer3_config/* primer3*settings.txt
+ dohtml primer3_manual.htm
+}
diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild
new file mode 100644
index 000000000000..9ba9ff0796c3
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.6.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+ if [[ ${CHOST} == *-darwin* ]]; then
+ sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+ fi
+
+ tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+ emake -C src
+}
+
+src_test () {
+ emake -C test | tee "${T}"/test.log
+ grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+ dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+ dodoc src/release_notes.txt example
+ insinto /opt/primer3_config
+ doins -r src/primer3_config/* primer3*settings.txt
+ dohtml primer3_manual.htm
+}
diff --git a/sci-biology/prints/Manifest b/sci-biology/prints/Manifest
new file mode 100644
index 000000000000..17763180d42d
--- /dev/null
+++ b/sci-biology/prints/Manifest
@@ -0,0 +1 @@
+DIST prints-39.0.tar.bz2 26277011 RMD160 15e50aadf48f55ea77eed159ac4892509b31e2d5 SHA1 27ebc398d2e2911aa50493cc4fb3354d1d258312 SHA256 671f870230424014d4b104b24adb13ad5a30f1d947d9565de4943f77dccb5187
diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml
new file mode 100644
index 000000000000..7d2927f1d2fb
--- /dev/null
+++ b/sci-biology/prints/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ A protein motif fingerprint database maintained at the University of
+ Manchester. A fingerprint is a group of conserved motifs used to
+ characterise a protein family; its diagnostic power is refined by
+ iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs
+ do not overlap, but are separated along a sequence, though they may be
+ contiguous in 3D-space. Fingerprints can encode protein folds and
+ functionalities more flexibly and powerfully than can single motifs,
+ full diagnostic potency deriving from the mutual context provided by
+ motif neighbours.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/prints/prints-39.0.ebuild b/sci-biology/prints/prints-39.0.ebuild
new file mode 100644
index 000000000000..c6dc22372252
--- /dev/null
+++ b/sci-biology/prints/prints-39.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+MY_PV="${PV/./_}"
+
+DESCRIPTION="A protein motif fingerprint database"
+HOMEPAGE="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="public-domain"
+IUSE="emboss minimal"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir PRINTS || die
+ echo
+ einfo "Indexing PRINTS for usage with EMBOSS."
+ EMBOSS_DATA="." printsextract -auto -infile prints${MY_PV}.dat || die \
+ "Indexing PRINTS failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins newpr.lis ${PN}${MY_PV}.{all.fasta,dat,kdat,lis,nam,vsn} || die \
+ "Installing raw database failed."
+ fi
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/PRINTS
+ doins PRINTS/* || die "Installing EMBOSS data files failed."
+ fi
+ dodoc README || die "Documentation installation failed."
+}
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
new file mode 100644
index 000000000000..1d0739662628
--- /dev/null
+++ b/sci-biology/probcons/Manifest
@@ -0,0 +1 @@
+DIST probcons_v1_12.tar.gz 43200 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
diff --git a/sci-biology/probcons/files/gcc-4.3.patch b/sci-biology/probcons/files/gcc-4.3.patch
new file mode 100644
index 000000000000..37c45c03a98f
--- /dev/null
+++ b/sci-biology/probcons/files/gcc-4.3.patch
@@ -0,0 +1,44 @@
+diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc
+--- probcons.orig/CompareToRef.cc 2008-04-08 16:38:46.000000000 -0700
++++ probcons/CompareToRef.cc 2008-04-08 16:39:41.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+
+diff -u probcons.orig/FixRef.cc probcons/FixRef.cc
+--- probcons.orig/FixRef.cc 2008-04-08 16:38:46.000000000 -0700
++++ probcons/FixRef.cc 2008-04-08 16:39:33.000000000 -0700
+@@ -17,6 +17,7 @@
+ #include <algorithm>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+
+diff -u probcons.orig/Main.cc probcons/Main.cc
+--- probcons.orig/Main.cc 2008-04-08 16:38:46.000000000 -0700
++++ probcons/Main.cc 2008-04-08 16:39:14.000000000 -0700
+@@ -21,6 +21,7 @@
+ #include <climits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+
+diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc
+--- probcons.orig/ProjectPairwise.cc 2008-04-08 16:38:46.000000000 -0700
++++ probcons/ProjectPairwise.cc 2008-04-08 16:39:25.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+
diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
new file mode 100644
index 000000000000..e07ebe1a613f
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
@@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index 75fc47a..4a19140 100644
+--- a/Makefile
++++ b/Makefile
+@@ -15,6 +15,8 @@ CXX = g++
+ # c) RELEASE mode
+ ################################################################################
+
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+
+ # debug mode
+@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+
+ ################################################################################
+ # 3) Dependencies
+@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot
+ all : $(TARGETS)
+
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+- $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm
+
+ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc
+
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+- $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc
+
+ project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc
+
+ makegnuplot : MakeGnuPlot.cc
+- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+
+ .PHONY : clean
+ clean:
diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
new file mode 100644
index 000000000000..1596f3b31916
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
@@ -0,0 +1,15 @@
+ SafeVector.h | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/SafeVector.h b/SafeVector.h
+index abf4b64..9c3292e 100644
+--- a/SafeVector.h
++++ b/SafeVector.h
+@@ -8,6 +8,7 @@
+ #ifndef SAFEVECTOR_H
+ #define SAFEVECTOR_H
+
++#include <cstddef>
+ #include <cassert>
+ #include <vector>
+
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/probcons/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild
new file mode 100644
index 000000000000..1b3e76cd92ba
--- /dev/null
+++ b/sci-biology/probcons/probcons-1.12-r1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}_v${PV/./_}"
+
+DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
+HOMEPAGE="http://probcons.stanford.edu/"
+SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+# Gnuplot is explicitly runtime-only, it's run using system()
+RDEPEND="
+ !sci-geosciences/gmt
+ sci-visualization/gnuplot"
+DEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-cxxflags.patch \
+ "${FILESDIR}"/gcc-4.3.patch \
+ "${FILESDIR}"/${P}-gcc-4.6.patch
+}
+
+src_compile() {
+ emake \
+ CXX="$(tc-getCXX)" \
+ OPT_CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin probcons project makegnuplot
+ # Overlap with imagemagick
+ newbin compare compare-probcons
+ dodoc README
+}
+
+pkg_postinst() {
+ ewarn "The 'compare' binary is installed as 'compare-probcons'"
+ ewarn "to avoid overlap with other packages."
+ einfo "You may also want to download the user manual"
+ einfo "from http://probcons.stanford.edu/manual.pdf"
+}
diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest
new file mode 100644
index 000000000000..c7ebb5b77b50
--- /dev/null
+++ b/sci-biology/prodigal/Manifest
@@ -0,0 +1,2 @@
+DIST prodigal.v2_50.tar.gz 496654 RMD160 335ef065f1b03c6e063172c1c7eb6343402ee8de SHA1 ca7f7a9fa8d2bf1b5a0965cde25385704c96bc4e SHA256 0220dcc740c49941f9c2536b3aa81d3193f885bfd05c694f805d90d2cefbc421
+DIST prodigal.v2_60.tar.gz 615326 RMD160 bcc876588dfc6fddd9e7c0a433347f8604d7db67 SHA1 23a45dafedd98c04f9a4edbe82b037120644eaa2 SHA256 f18b093e0ac3b9ba40fc4d7bb76c2e20f2edb6d265451c82e3396138c9aac331
diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml
new file mode 100644
index 000000000000..6e8b2ee66e66
--- /dev/null
+++ b/sci-biology/prodigal/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="google-code">prodigal</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/prodigal/prodigal-2.50.ebuild b/sci-biology/prodigal/prodigal-2.50.ebuild
new file mode 100644
index 000000000000..8e28c0a24196
--- /dev/null
+++ b/sci-biology/prodigal/prodigal-2.50.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm"
+HOMEPAGE="http://prodigal.ornl.gov/ http://code.google.com/p/prodigal/"
+SRC_URI="http://prodigal.googlecode.com/files/prodigal.v${MY_PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/prodigal.v${MY_PV}"
+
+src_prepare() {
+ sed -i -e 's/CFLAGS=/CFLAGS+=/' -e 's/LDFLAGS=/LDFLAGS+=/' Makefile || die
+}
+
+src_install() {
+ dobin prodigal
+ dodoc README CHANGES
+}
diff --git a/sci-biology/prodigal/prodigal-2.60.ebuild b/sci-biology/prodigal/prodigal-2.60.ebuild
new file mode 100644
index 000000000000..21c788eaccff
--- /dev/null
+++ b/sci-biology/prodigal/prodigal-2.60.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm"
+HOMEPAGE="http://prodigal.ornl.gov/ http://code.google.com/p/prodigal/"
+SRC_URI="http://prodigal.googlecode.com/files/prodigal.v${MY_PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/prodigal.v${MY_PV}"
+
+src_prepare() {
+ sed -i -e 's/CFLAGS=/CFLAGS+=/' -e 's/LDFLAGS=/LDFLAGS+=/' Makefile || die
+}
+
+src_install() {
+ dobin prodigal
+ dodoc README CHANGES
+}
diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
new file mode 100644
index 000000000000..386263860516
--- /dev/null
+++ b/sci-biology/profphd/Manifest
@@ -0,0 +1,2 @@
+DIST profphd-1.0.39.tar.xz 4406776 SHA256 4ff67e7b4dcb5748ee5115f1e7b9de7de6ca1c5a7982971a7147fe4ee5a5d288 SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b WHIRLPOOL 7e149f3e724ae5e727810ace6a1063708c35bb957861e4873c0763e48af5362ea50757d94c592052fec9d6e63767d036a39104a72ba6deb981c1f6023f19464e
+DIST profphd-1.0.40.tar.xz 4491592 SHA256 50c85da552993758df191e3e06910fb221a156a8eaba94badf5a716b04648c5c SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 WHIRLPOOL 4d7ac3cf32607cefc983116fa8fe8e795e92e89590bd612a2180e9fd59ec5c60220b065a2fddf3552aa81a3d02f852a36e08086d0867ac28ded2faf0d31a38ad
diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
new file mode 100644
index 000000000000..10682271601c
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
@@ -0,0 +1,16 @@
+ src/prof/prof | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/prof/prof b/src/prof/prof
+index 4f26024..356442d 100755
+--- a/src/prof/prof
++++ b/src/prof/prof
+@@ -238,7 +238,7 @@ See each keyword for more help. Most of these are likely to be broken.
+
+ alternative connectivity patterns (default=3)
+
+-=item 3
++=item C<3>
+
+ predict sec + acc + htm
+
diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/profphd/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
new file mode 100644
index 000000000000..8deb4f87abae
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.39.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+ dev-perl/librg-utils-perl
+ sci-libs/profnet
+ sci-libs/profphd-utils
+"
+
+src_prepare() {
+ sed \
+ -e '/ln -s/s:prof$:profphd:g' \
+ -i src/prof/Makefile || die
+ epatch "${FILESDIR}"/${P}-perl.patch
+}
+
+src_compile() {
+ emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+ emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
new file mode 100644
index 000000000000..518ab5f1e473
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+ dev-perl/librg-utils-perl
+ sci-libs/profnet
+ sci-libs/profphd-utils
+"
+
+src_prepare() {
+ sed \
+ -e '/ln -s/s:prof$:profphd:g' \
+ -i src/prof/Makefile || die
+ epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
+}
+
+src_compile() {
+ emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+ emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}
diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest
new file mode 100644
index 000000000000..abbafda0a493
--- /dev/null
+++ b/sci-biology/prosite/Manifest
@@ -0,0 +1,4 @@
+DIST prosite-19.36.tar.bz2 4462981 RMD160 4d80651193b4c34bfdf42b770d4ec07927666057 SHA1 52acc49f0452b344a20b52983cbd896b6dd3b79b SHA256 6f923d4794f50c8e68d030d01cb6675579007cc04c197d811886dfb4ae853607
+DIST prosite-20.36.tar.bz2 5953220 RMD160 51f2da1efc886616e78ebced1a32c3a916bdef8f SHA1 328518c8e936d8960846bdefa8164a6f78a73503 SHA256 05593ff424d4145e19a7f394dab5a64fe0c5c6a640091fe03451f52bd31bfd25
+DIST prosite-20.52.tar.bz2 7038156 RMD160 506a64a15ea1145eadb8138b192718436282a2c1 SHA1 39abf5053c21f3d03ce0bb0bfc1fb3fb82284fb6 SHA256 89e5fc11e2ed18b1f16cc78e5271cccf6a5ea28a64fdcd7e99a770dfebb1968d
+DIST prosite-20.72.tar.bz2 7521700 RMD160 5f48b403a05caeebf4136c2a626fa7a31e413b27 SHA1 164bc5ffc41aa2eb7e0a8588af577b84eca82040 SHA256 93b8664adecce63b14a96b6b9fbd970bcc2852a83413fd9b873df84dcfe07d12
diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml
new file mode 100644
index 000000000000..075d4b7bcf10
--- /dev/null
+++ b/sci-biology/prosite/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ A protein families and domains database maintained at the Swiss
+ Institude for Bioinformatics. It consists of biologically significant
+ sites, patterns and profiles that help to reliably identify to which
+ known protein family (if any) a new sequence belongs. PROSITE currently
+ contains patterns and profiles specific for more than a thousand
+ protein families or domains. Each of these signatures comes with
+ documentation providing background information on the structure and
+ function of these proteins.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/prosite/prosite-19.36.ebuild b/sci-biology/prosite/prosite-19.36.ebuild
new file mode 100644
index 000000000000..552c9193733f
--- /dev/null
+++ b/sci-biology/prosite/prosite-19.36.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A protein families and domains database"
+LICENSE="swiss-prot"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir PROSITE
+ echo
+ einfo "Indexing PROSITE for usage with EMBOSS."
+ EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+ "Indexing PROSITE failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins ${PN}.{doc,dat,lis} || die "Installing raw database failed."
+ fi
+ dodoc *.txt || die "Documentation installation failed."
+ dohtml *.htm || die "HTML documentation installation failed."
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/PROSITE
+ doins PROSITE/* || die "Installing EMBOSS data files failed."
+ fi
+}
diff --git a/sci-biology/prosite/prosite-20.36.ebuild b/sci-biology/prosite/prosite-20.36.ebuild
new file mode 100644
index 000000000000..9bb65805bd27
--- /dev/null
+++ b/sci-biology/prosite/prosite-20.36.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A protein families and domains database"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="swiss-prot"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ~ppc x86"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir PROSITE
+ echo
+ einfo "Indexing PROSITE for usage with EMBOSS."
+ EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+ "Indexing PROSITE failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins *.{doc,dat} || die "Installing raw database failed."
+ fi
+ insinto /usr/share/doc/${PF}
+ doins *.pdf || die "PDF documentation installation failed."
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/PROSITE
+ doins PROSITE/* || die "Installing EMBOSS data files failed."
+ fi
+}
diff --git a/sci-biology/prosite/prosite-20.52.ebuild b/sci-biology/prosite/prosite-20.52.ebuild
new file mode 100644
index 000000000000..69a997ed0987
--- /dev/null
+++ b/sci-biology/prosite/prosite-20.52.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A protein families and domains database"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="swiss-prot"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir PROSITE
+ echo
+ einfo "Indexing PROSITE for usage with EMBOSS."
+ EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+ "Indexing PROSITE failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins *.{doc,dat} || die "Installing raw database failed."
+ fi
+ insinto /usr/share/doc/${PF}
+ doins *.pdf || die "PDF documentation installation failed."
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/PROSITE
+ doins PROSITE/* || die "Installing EMBOSS data files failed."
+ fi
+}
diff --git a/sci-biology/prosite/prosite-20.72.ebuild b/sci-biology/prosite/prosite-20.72.ebuild
new file mode 100644
index 000000000000..799a5a432c14
--- /dev/null
+++ b/sci-biology/prosite/prosite-20.72.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A protein families and domains database"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="swiss-prot"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ if use emboss; then
+ mkdir PROSITE
+ echo
+ einfo "Indexing PROSITE for usage with EMBOSS."
+ EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+ "Indexing PROSITE failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins *.{doc,dat} || die "Installing raw database failed."
+ fi
+ insinto /usr/share/doc/${PF}
+ doins *.pdf || die "PDF documentation installation failed."
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/PROSITE
+ doins PROSITE/* || die "Installing EMBOSS data files failed."
+ fi
+}
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
new file mode 100644
index 000000000000..1c17d7b94a74
--- /dev/null
+++ b/sci-biology/psipred/Manifest
@@ -0,0 +1,7 @@
+DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34
+DIST psipred3.4.tar.gz 1102416 SHA256 c0eb8877313eb0564d34fc4d0e2d8d22e09d84d245e41008227560a10e64da9d SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 WHIRLPOOL bdb47f296db1172df08f84b8cf18782e8585a8bc49f190b9783192db0e9d632bd6660437e8a35c24bb5970ca7a556b368c5a93373772f20d4be9a98ef963b902
+DIST psipred3.5.tar.gz 1101579 SHA256 107979a6bee968ba1df1ac1ee63bc1611105b83a7d519ab814f848ed955b76d8 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 WHIRLPOOL fb07fdf550af6c9942e131a4856942c74adb3a7954c433ac7bc27680d9ab2b3db82a5178a15bcea224f7bb0da3cd84c94a4e9188be4fcbd49851037f631732e3
+DIST psipred31.tar.gz 746797 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd SHA512 a04482fc5a08de03b2c1ac3eafbc289d476906811ef2557681f00e3ba865488c6061a194c5e12fe3ff38d31f42f13f4e783de1ca4a04508dd38a93c3ad848710 WHIRLPOOL 288d161698726a944b40acb3e2c355e61bad3644bf5edca40fd5e478f9d37e3acc9a91ee199fbadea680ab3a8c974eb8f80dd700dfe790e84d8a862148538dff
+DIST psipred32.tar.gz 747120 SHA256 0775b0f07df87b2afd4989a378fc9b47f462507a264aaf2d56dd0243d9d00343 SHA512 49660d1c3cb9aa4c3ab13e721e23b83d70d0b6ecb772b08bd1058d3293dbcc9642d63092dd9746aa2a3a9085a13ba91e9849172d36954228a4f7a16e6e81050d WHIRLPOOL 24413200771fcee89c123fad25033b3230de3fdd82016ad7d084ddb096c081c46537f35c06578dad84a79a62c493e03b8f7b51be296b04d9568ea00b94293360
+DIST psipred321.tar.gz 747151 SHA256 5e88f2402e333be401b3022937b0167a33203f6289a84dd344941546f550f1f8 SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1 WHIRLPOOL bb7111851ffe533b30fd6b77fb1ae396f0dd6506ce941944974c3b5c73c41d1a5b04c5af3d7e697aeb0640c03168b78d8832747940ed0de087df784d2d27e9f1
+DIST tdbdata.tar.gz 40241247 SHA256 87b7743538898f6cdf89cc5c18e1ecd040bc6223a01821d2bfc3109f4571851f SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c WHIRLPOOL 37bc0912c6a71d1396489161465c690fb63d28167694d2e43553b6684c1f1f88866b2bf71f9531c7a7f41fc8ca81a6c93c2895ed498a07e3c4836f8c8bf4a34e
diff --git a/sci-biology/psipred/files/2.6.1-Makefile.patch b/sci-biology/psipred/files/2.6.1-Makefile.patch
new file mode 100644
index 000000000000..0a6df743ec83
--- /dev/null
+++ b/sci-biology/psipred/files/2.6.1-Makefile.patch
@@ -0,0 +1,42 @@
+--- src/Makefile 2008-03-09 22:59:51.000000000 +0100
++++ src/Makefile.new 2009-04-09 12:31:38.669457918 +0200
+@@ -6,9 +6,7 @@
+ #### CFLAGS Flags to pass to C compiler.
+
+ INCDIR = .
+-CC = cc
+
+-CFLAGS = -O
+ LIBS = -lm
+
+ all: psipred psipass2 seq2mtx pfilt
+@@ -20,13 +18,13 @@
+ /bin/rm -f psipred psipass2 seq2mtx pfilt
+
+ psipred: sspred_avpred.c ssdefs.h sspred_net.h
+- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
+
+ psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h
+- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
+
+ seq2mtx: seq2mtx.c
+- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
++ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
+
+ pfilt: pfilt.c
+- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
++ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
+--- src/Makefile 2009-04-09 12:34:41.636939862 +0200
++++ src/Makefile.new 2009-04-09 12:36:03.796098341 +0200
+@@ -12,7 +12,8 @@
+ all: psipred psipass2 seq2mtx pfilt
+
+ install:
+- /bin/cp psipred psipass2 seq2mtx pfilt ../bin
++ /bin/mkdir -p $(DESTDIR)/usr/bin
++ /bin/cp psipred psipass2 seq2mtx pfilt $(DESTDIR)/usr/bin
+
+ clean:
+ /bin/rm -f psipred psipass2 seq2mtx pfilt
diff --git a/sci-biology/psipred/files/2.6.1-path.patch b/sci-biology/psipred/files/2.6.1-path.patch
new file mode 100644
index 000000000000..9b8d6b9fecfa
--- /dev/null
+++ b/sci-biology/psipred/files/2.6.1-path.patch
@@ -0,0 +1,34 @@
+--- runpsipred 2008-04-05 00:14:36.000000000 +0200
++++ runpsipred.new 2009-04-09 12:40:46.376203036 +0200
+@@ -14,13 +14,13 @@
+ set dbname = nr
+
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V2 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V2 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
+--- runpsipred_single 2008-04-05 00:14:38.000000000 +0200
++++ runpsipred_single.new 2009-04-09 12:41:10.086067082 +0200
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+
+ # Where the PSIPRED V2 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V2 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.0-path.patch b/sci-biology/psipred/files/3.0-path.patch
new file mode 100644
index 000000000000..ebf9b2a61f4e
--- /dev/null
+++ b/sci-biology/psipred/files/3.0-path.patch
@@ -0,0 +1,38 @@
+diff --git a/runpsipred b/runpsipred
+index e133686..6ad57cc 100755
+--- a/runpsipred
++++ b/runpsipred
+@@ -14,13 +14,13 @@
+ set dbname = uniref90
+
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V3 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
+diff --git a/runpsipred_single b/runpsipred_single
+index 1f7680b..7bd5bc3 100755
+--- a/runpsipred_single
++++ b/runpsipred_single
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V3 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch
new file mode 100644
index 000000000000..0c70b6868565
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-Makefile.patch
@@ -0,0 +1,38 @@
+diff --git a/src/Makefile b/src/Makefile
+index abed8af..26061fa 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,9 +6,9 @@
+ #### CFLAGS Flags to pass to C compiler.
+
+ INCDIR = .
+-CC = cc
++CC ?= gcc
+
+-CFLAGS = -O
++CFLAGS ?= -O2
+ LIBS = -lm
+
+ all: psipred psipass2 chkparse seq2mtx pfilt
+@@ -20,16 +20,16 @@ clean:
+ /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt
+
+ psipred: sspred_avpred.c ssdefs.h sspred_net.h
+- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
+
+ psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h
+- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
+
+ chkparse: chkparse.c
+- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse
++ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse
+
+ seq2mtx: seq2mtx.c
+- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
++ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
+
+ pfilt: pfilt.c
+- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
++ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
diff --git a/sci-biology/psipred/files/3.1-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch
new file mode 100644
index 000000000000..e58d677258e0
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 4d8e5ff..0d82483 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -213,7 +213,7 @@ predict(int argc, char **argv)
+ int getmtx(FILE *lfil)
+ {
+ int aa, i, j, naa;
+- char buf[256], *p;
++ char buf[65536], *p;
+
+ if (fscanf(lfil, "%d", &naa) != 1)
+ fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch
new file mode 100644
index 000000000000..564e9c8a1ef9
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-path.patch
@@ -0,0 +1,38 @@
+diff --git a/runpsipred b/runpsipred
+index 4ccf44e..34dee99 100755
+--- a/runpsipred
++++ b/runpsipred
+@@ -14,13 +14,13 @@
+ set dbname = uniref90filt
+
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V2 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V2 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
+diff --git a/runpsipred_single b/runpsipred_single
+index 1f7680b..7bd5bc3 100755
+--- a/runpsipred_single
++++ b/runpsipred_single
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+
+ # Where the PSIPRED V3 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+
+ set basename = $1:r
+ set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch
new file mode 100644
index 000000000000..ec06d141ee34
--- /dev/null
+++ b/sci-biology/psipred/files/3.2-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 37b1332..4f04ab6 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -223,7 +223,7 @@ predict(int argc, char **argv)
+ int getmtx(FILE *lfil)
+ {
+ int aa, i, j, naa;
+- char buf[256], *p;
++ char buf[65536], *p;
+
+ if (fscanf(lfil, "%d", &naa) != 1)
+ fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
new file mode 100644
index 000000000000..655b161c218d
--- /dev/null
+++ b/sci-biology/psipred/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.1.ebuild b/sci-biology/psipred/psipred-3.1.ebuild
new file mode 100644
index 000000000000..b81c4149b568
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils prefix toolchain-funcs versionator
+
+MY_P="${PN}$(delete_all_version_separators)"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/${PV}-Makefile.patch \
+ "${FILESDIR}"/${PV}-path.patch \
+ "${FILESDIR}"/${PV}-fgets.patch
+ eprefixify runpsipred*
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC) || die "emake failed"
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install || die "installation failed"
+ dobin runpsipred* bin/* BLAST+/runpsipred* || die
+ insinto /usr/share/${PN}
+ doins -r data || die "failed to install data"
+ dodoc README || die "nothing to read"
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild
new file mode 100644
index 000000000000..6b2158ef81e9
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.2.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils prefix toolchain-funcs versionator
+
+MY_P="${PN}$(delete_all_version_separators)"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/3.1-Makefile.patch \
+ "${FILESDIR}"/3.1-path.patch \
+ "${FILESDIR}"/3.2-fgets.patch
+ eprefixify runpsipred*
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install
+ dobin runpsipred* bin/* BLAST+/runpsipred*
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc README
+ newdoc BLAST+/README README-blast
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.2.ebuild b/sci-biology/psipred/psipred-3.2.ebuild
new file mode 100644
index 000000000000..418179c41278
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils prefix toolchain-funcs versionator
+
+MY_P="${PN}$(delete_all_version_separators)"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/3.1-Makefile.patch \
+ "${FILESDIR}"/3.1-path.patch \
+ "${FILESDIR}"/${PV}-fgets.patch
+ eprefixify runpsipred*
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC) || die "emake failed"
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install || die "installation failed"
+ dobin runpsipred* bin/* BLAST+/runpsipred* || die
+ insinto /usr/share/${PN}
+ doins -r data || die "failed to install data"
+ dodoc README || die "nothing to read"
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild
new file mode 100644
index 000000000000..3727fc29ad25
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.3.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+ http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+ test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/3.1-Makefile.patch \
+ "${FILESDIR}"/3.1-path.patch \
+ "${FILESDIR}"/3.2-fgets.patch
+ eprefixify runpsipred*
+ emake -C src clean
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install
+ dobin runpsipred* bin/* BLAST+/runpsipred*
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc README
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
new file mode 100644
index 000000000000..95d859b7898d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+ http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+ test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+ app-shells/tcsh
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/3.1-Makefile.patch \
+ "${FILESDIR}"/3.1-path.patch \
+ "${FILESDIR}"/3.2-fgets.patch
+ eprefixify runpsipred*
+ emake -C src clean
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install
+ dobin runpsipred* bin/* BLAST+/runpsipred*
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc README
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild
new file mode 100644
index 000000000000..95d859b7898d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.5.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+ http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+ test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+ app-shells/tcsh
+ sci-biology/ncbi-tools
+ || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+ rm -f bin/*
+ epatch \
+ "${FILESDIR}"/3.1-Makefile.patch \
+ "${FILESDIR}"/3.1-path.patch \
+ "${FILESDIR}"/3.2-fgets.patch
+ eprefixify runpsipred*
+ emake -C src clean
+}
+
+src_compile() {
+ emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+ emake -C src DESTDIR="${D}" install
+ dobin runpsipred* bin/* BLAST+/runpsipred*
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc README
+}
+
+pkg_postinst() {
+ elog "Please use the update_blastdb.pl in order to"
+ elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
new file mode 100644
index 000000000000..4aea08f2d664
--- /dev/null
+++ b/sci-biology/pysam/Manifest
@@ -0,0 +1 @@
+DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 000000000000..49afc3c3d532
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="google-code">pysam</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/pysam/pysam-0.6-r1.ebuild b/sci-biology/pysam/pysam-0.6-r1.ebuild
new file mode 100644
index 000000000000..3873100fa45f
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.6-r1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam"
+SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_compile() {
+ python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
+ distutils-r1_python_compile
+}
diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest
new file mode 100644
index 000000000000..b939f54fb27d
--- /dev/null
+++ b/sci-biology/qrna/Manifest
@@ -0,0 +1 @@
+DIST qrna-2.0.3c.tar.bz2 6423705 SHA256 fc88b58dddab26f20477a50340453e9d360ea34956ba526f7db6959283399b1c SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 WHIRLPOOL f7c788629f6580e3f1c2ccaa5109ba13d8f103abfd3a88f3ef127577fc825fdc7deef102325ab2645a24ba1215d59b21e2c77448631c90d6eae47aa95a9463e5
diff --git a/sci-biology/qrna/files/26qrna b/sci-biology/qrna/files/26qrna
new file mode 100644
index 000000000000..53a90b90ed78
--- /dev/null
+++ b/sci-biology/qrna/files/26qrna
@@ -0,0 +1 @@
+QRNADB="/usr/share/qrna/data"
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch
new file mode 100644
index 000000000000..dfa1b2a29e94
--- /dev/null
+++ b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch
@@ -0,0 +1,328 @@
+diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c
+--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300
++++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300
+@@ -215,7 +215,7 @@
+ }
+
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ readline(V->f, V->sbuffer);
+ }
+@@ -277,7 +277,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -305,7 +305,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -314,7 +314,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -323,7 +323,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -337,7 +337,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -355,7 +355,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -367,7 +367,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -389,7 +389,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -398,7 +398,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -416,7 +416,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -427,7 +427,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -460,11 +460,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -494,12 +494,12 @@
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+- getline(V); /*skip title-junk line*/
++ get_line(V); /*skip title-junk line*/
+
+ readLoop(0, endNBRF, V);
+
+ while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -529,7 +529,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -549,7 +549,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -571,7 +571,7 @@
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -598,7 +598,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -607,7 +607,7 @@
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -631,7 +631,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -647,7 +647,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -658,7 +658,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -680,7 +680,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -692,7 +692,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -700,7 +700,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -732,14 +732,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -747,7 +747,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -786,7 +786,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -800,7 +800,7 @@
+ SeqfilePosition(SQFILE *sqfp, long offset)
+ {
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -817,7 +817,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -912,7 +912,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
+@@ -991,7 +991,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
+@@ -1098,7 +1098,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
+@@ -1204,7 +1204,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
new file mode 100644
index 000000000000..d03f650dd39e
--- /dev/null
+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
@@ -0,0 +1,28 @@
+diff --git a/src/Makefile b/src/Makefile
+index 1d1631b..4fa3af9 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -131,17 +131,17 @@ DEMOS =
+ all: $(PROGS)
+
+ main: $(OBJ) main.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
+ cfgbuild: $(OBJ) cfgbuild.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna: $(OBJ) eqrna.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna_sample: $(OBJ) eqrna_sample.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ shuffle: $(OBJ) shuffle.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ rnamat_main: $(OBJ2) rnamat_main.o
+- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
+
+ main.o: ../src/main.c
+ $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml
new file mode 100644
index 000000000000..d4648212cbad
--- /dev/null
+++ b/sci-biology/qrna/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/qrna/qrna-2.0.3c-r1.ebuild b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
new file mode 100644
index 000000000000..f8834630acee
--- /dev/null
+++ b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Prototype ncRNA genefinder"
+HOMEPAGE="http://selab.janelia.org/software.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86"
+IUSE=""
+
+RDEPEND="
+ dev-lang/perl
+ sci-biology/hmmer"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-glibc-2.10.patch \
+ "${FILESDIR}"/${P}-ldflags.patch
+ sed \
+ -e "s:^CC.*:CC = $(tc-getCC):" \
+ -e "/^AR/s:ar:$(tc-getAR):g" \
+ -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \
+ -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \
+ -i {src,squid,squid02}/Makefile || die
+ rm -v squid*/*.a
+}
+
+src_compile() {
+ local dir
+ for dir in squid squid02 src; do
+ emake -C ${dir}
+ done
+}
+
+src_install () {
+ dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/*
+
+ newdoc 00README README
+ insinto /usr/share/doc/${PF}
+ doins documentation/*
+
+ insinto /usr/share/${PN}/data
+ doins lib/*
+ insinto /usr/share/${PN}/demos
+ doins Demos/*
+
+ # Sets the path to the QRNA data files.
+ doenvd "${FILESDIR}"/26qrna
+}
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
new file mode 100644
index 000000000000..7e64fe420af6
--- /dev/null
+++ b/sci-biology/raxml/Manifest
@@ -0,0 +1 @@
+DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 WHIRLPOOL 7fe7ac66412c979d3ecca17e2c06a32566fefe7bdcf39664a0885fcdebc2b8187c222ca5e29cf2685085fba21a8aff0a2aefceec08823cab155a5f62f8b59490
diff --git a/sci-biology/raxml/files/raxml-7.2.5-makefile.patch b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
new file mode 100644
index 000000000000..8b381e50cb58
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 8d09549..59af556 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+
+-CC = gcc
++CC ?= gcc
+
+
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2
++CFLAGS += -D_GNU_SOURCE
+ #-Wall -std=c99 -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -pedantic-errors -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+
+
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+
+ raxmlHPC : $(objs)
+- $(CC) -o raxmlHPC $(objs) $(LIBRARIES)
++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
+
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
new file mode 100644
index 000000000000..ae83e2eef4e7
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc | 6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 716b6c6..f0c1de2 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+
+-CC = gcc
++CC ?= gcc
+
+
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse
++CFLAGS += -D_GNU_SOURCE
+
+
+
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+
+ raxmlHPC : $(objs)
+- $(CC) -o raxmlHPC $(objs) $(LIBRARIES)
++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
+
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/raxml/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
new file mode 100644
index 000000000000..b9ace2a0ec0f
--- /dev/null
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
+HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
+SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse3 +threads"
+
+REQUIRED_USE="cpu_flags_x86_sse3"
+
+# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
+DEPEND="" # mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/RAxML-${PV}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-makefile.patch
+
+ use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3
+ use threads && \
+ append-cflags -D_USE_PTHREADS && \
+ append-ldflags -pthread
+
+ tc-export CC
+}
+
+src_compile() {
+ emake -f Makefile.gcc
+}
+
+src_install() {
+ dobin raxmlHPC
+}
diff --git a/sci-biology/readseq/Manifest b/sci-biology/readseq/Manifest
new file mode 100644
index 000000000000..bcd1dfa237bf
--- /dev/null
+++ b/sci-biology/readseq/Manifest
@@ -0,0 +1,2 @@
+DIST readseq-20100513.zip 628406 SHA256 878b689828bdf59a73c377c314fe504b9f18569ed5cd512acdb264cf90e72601 SHA512 6e2a2207e3a1f14e5cc4f7ffd2c74563b6deb088dda02727611359a17e1b157d9c661715d1f896d1573786cb88f61d3b952ab7a53e6dc30f2dcbcead58604b32 WHIRLPOOL 6f5b7ff075a081f521971689d014ad3ea6ffdc50db1b24766712d21fb86f83d7767f9afa76473f0be6f36560c8572c7051337cde8020cb9562dfef96a2bfdc8a
+DIST readseq-source-20080420.zip 627341 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd SHA512 cbc7afa46d2f0cfb30aa75ab88e4942a18ddf46a03a4cfb8d7e07bd23bce3fe015483899d371b947a0f1d6ec464b8c1238df7f7fc89753bb75dbb284f1e07b48 WHIRLPOOL fb180c53cb0555887d5278871498d66840d1d27da47ef6a947f0cd048bfb79762faf9493a645be6909bf41c5627131f3ced8d29b8241372d1e6034dc7524004d
diff --git a/sci-biology/readseq/files/20080420-no-bundling.patch b/sci-biology/readseq/files/20080420-no-bundling.patch
new file mode 100644
index 000000000000..f2e1708f8821
--- /dev/null
+++ b/sci-biology/readseq/files/20080420-no-bundling.patch
@@ -0,0 +1,14 @@
+diff --git a/build.xml b/build.xml
+index e3d723c..4b44d6f 100644
+--- a/build.xml
++++ b/build.xml
+@@ -229,9 +229,6 @@
+
+ <!-- for now, unjar xml classes into build/classes and rejar in readseq.jar -->
+
+- <unjar overwrite="false" src="${orgxml.jar}" dest="${build.home}/classes" />
+- <unjar overwrite="false" src="${xml.jar}" dest="${build.home}/classes" />
+-
+ <!-- <copy todir="${build.home}/classes""> -->
+ <!-- <src dir="${basedir}/META-INF"/> -->
+ <!-- </copy> -->
diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml
new file mode 100644
index 000000000000..b198f044f3f5
--- /dev/null
+++ b/sci-biology/readseq/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ Reads and writes nucleic/protein sequences in various formats. Data
+ files may have multiple sequences.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/readseq/readseq-20080420-r1.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild
new file mode 100644
index 000000000000..43c538beb596
--- /dev/null
+++ b/sci-biology/readseq/readseq-20080420-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}-source-${PV}"
+DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
+HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
+# Originally unversioned at
+# http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip.
+# Renamed to the date of the modification and mirrored
+SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="!=sci-biology/meme-4.8.1
+ >=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+ app-arch/unzip"
+
+S=${WORKDIR}
+
+java_prepare() {
+ rm "${S}"/lib/* || die
+ epatch "${FILESDIR}"/${PV}-*
+}
+
+src_install() {
+ java-pkg_dojar build/readseq.jar
+ java-pkg_dolauncher
+}
+
+pkg_postinst() {
+ elog "Documentation is available at"
+ elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
+}
diff --git a/sci-biology/readseq/readseq-20100513.ebuild b/sci-biology/readseq/readseq-20100513.ebuild
new file mode 100644
index 000000000000..6539ebd427cc
--- /dev/null
+++ b/sci-biology/readseq/readseq-20100513.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
+HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
+SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="!=sci-biology/meme-4.8.1
+ >=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+ app-arch/unzip"
+
+S=${WORKDIR}
+
+java_prepare() {
+ rm "${S}"/lib/* || die
+ epatch "${FILESDIR}"/20080420-*
+}
+
+src_install() {
+ java-pkg_dojar build/readseq.jar
+ java-pkg_dolauncher
+}
+
+pkg_postinst() {
+ elog "Documentation is available at"
+ elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html"
+}
diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest
new file mode 100644
index 000000000000..632fbeb3bc72
--- /dev/null
+++ b/sci-biology/rebase/Manifest
@@ -0,0 +1,2 @@
+DIST rebase-1507.tar.xz 68538212 SHA256 87880a3f8cd49f537abf0a3d3fe00dca928ab5299cfd436351a279051f358efe SHA512 9fcb61d0f53f227485ecdaa86709b3fb7c20d8a430c456d2c24f68154691028709358d8dc25d4be2662d368e3cdd13d15eb316342dfb0f1aa8447b3742b80375 WHIRLPOOL f8cfc127890e17529d557f69c20be7ad90cd9e01ff9e112d41bb8c88359f7310744977253e8f82c71301ef1ea449f2e4cee9189e3b552edc242ab1033dca0b5e
+DIST rebase-1508.tar.xz 69944352 SHA256 579ef686b0efea32d88633f85411da9c1396572eec0d20bd163ca7bf615c7b04 SHA512 d5dc9eb704ce28ab7951ab2a8781de76dcbd7a4b6d6c6634abcd36766c8dce77b6d8a712789fe6293a6ddc66cd9103e17121b0ff52f0d3fbabfc5bf47c2f2100 WHIRLPOOL f082a3096cef636a61a176d3d3fe5b993bc83e3b332d134ebc20201d21f2f66e3400ffc5d561018c63fb3201c5fc0862126a32c17c5c96f118859b62a618d341
diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml
new file mode 100644
index 000000000000..734fcff7e215
--- /dev/null
+++ b/sci-biology/rebase/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ The Restriction Enzyme data BASE is a collection of information about
+ restriction enzymes and related proteins. It is maintained by New
+ England Biolabs. It contains published and unpublished references,
+ recognition and cleavage sites, isoschizomers, commercial availability,
+ methylation sensitivity, crystal and sequence data. DNA
+ methyltransferases, homing endonucleases, nicking enzymes, specificity
+ subunits and control proteins are also included. More recently,
+ putative DNA methyltransferases and restriction enzymes, as predicted
+ from analysis of genomic sequences, are also listed.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/rebase/rebase-1507.ebuild b/sci-biology/rebase/rebase-1507.ebuild
new file mode 100644
index 000000000000..6b32ba231a2e
--- /dev/null
+++ b/sci-biology/rebase/rebase-1507.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PV=${PV#1}
+
+DESCRIPTION="A restriction enzyme database"
+HOMEPAGE="http://rebase.neb.com"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
+IUSE="emboss minimal"
+
+RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+ if use emboss; then
+ echo; einfo "Indexing Rebase for usage with EMBOSS."
+ mkdir REBASE || die
+ EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
+ -protofile proto.${MY_PV} -equivalences \
+ || die "Indexing Rebase failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins withrefm.${MY_PV} proto.${MY_PV}
+ fi
+ newdoc REBASE.DOC README
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/REBASE
+ doins REBASE/embossre.{enz,ref,sup}
+ insinto /usr/share/EMBOSS/data
+ doins REBASE/embossre.equ
+ fi
+}
diff --git a/sci-biology/rebase/rebase-1508.ebuild b/sci-biology/rebase/rebase-1508.ebuild
new file mode 100644
index 000000000000..f171a569ee83
--- /dev/null
+++ b/sci-biology/rebase/rebase-1508.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PV=${PV#1}
+
+DESCRIPTION="A restriction enzyme database"
+HOMEPAGE="http://rebase.neb.com"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
+IUSE="emboss minimal"
+
+RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+ if use emboss; then
+ echo; einfo "Indexing Rebase for usage with EMBOSS."
+ mkdir REBASE || die
+ EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
+ -protofile proto.${MY_PV} -equivalences \
+ || die "Indexing Rebase failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}
+ doins withrefm.${MY_PV} proto.${MY_PV}
+ fi
+ newdoc REBASE.DOC README
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data/REBASE
+ doins REBASE/embossre.{enz,ref,sup}
+ insinto /usr/share/EMBOSS/data
+ doins REBASE/embossre.equ
+ fi
+}
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
new file mode 100644
index 000000000000..d779bd4735c4
--- /dev/null
+++ b/sci-biology/recon/Manifest
@@ -0,0 +1 @@
+DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec
diff --git a/sci-biology/recon/files/1.06-buffer-overflow.patch b/sci-biology/recon/files/1.06-buffer-overflow.patch
new file mode 100644
index 000000000000..29d220c7310d
--- /dev/null
+++ b/sci-biology/recon/files/1.06-buffer-overflow.patch
@@ -0,0 +1,13 @@
+diff --git a/src/eledef.c b/src/eledef.c
+index 964890b..a001ec4 100644
+--- a/src/eledef.c
++++ b/src/eledef.c
+@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
+
+ void img_charge(IPROT_t **shadow, int ct, FILE *input) {
+ int i=0, pos=0;
+- char line[100];
++ char line[256];
+ int scan_flag;
+ MSP_t msp;
+
diff --git a/sci-biology/recon/files/recon-1.06-respect.patch b/sci-biology/recon/files/recon-1.06-respect.patch
new file mode 100644
index 000000000000..a02038d84784
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.06-respect.patch
@@ -0,0 +1,24 @@
+ src/Makefile | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index 36ef59b..e45a0f2 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -13,14 +13,14 @@ MANDIR = $(HOME)/man
+ #SRCDIR = .
+
+ ## your compiler
+-CC = gcc
++CC ?= gcc
+ #CC = cc # for SGI Origin200 compiler#
+
+ ## any special compiler flags you want
+ # -pedantic clashes with -DMEMDEBUG??
+ #
+ #CFLAGS = -g -Wall -pedantic
+-CFLAGS = -O
++CFLAGS ?= -O
+ #CFLAGS = -g
+ #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
+
diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/recon/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/recon/recon-1.06-r1.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild
new file mode 100644
index 000000000000..86e820f49e9f
--- /dev/null
+++ b/sci-biology/recon/recon-1.06-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit eutils
+
+DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
+HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
+SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="examples"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/RECON${PV}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-buffer-overflow.patch
+ sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
+}
+
+src_compile() {
+ emake -C src
+}
+
+src_install() {
+ dobin scripts/*
+ exeinto /usr/libexec/${PN}
+ doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
+ dodoc 00README
+ insinto /usr/share/${PN}
+ use examples && doins -r Demos
+}
diff --git a/sci-biology/recon/recon-1.06-r2.ebuild b/sci-biology/recon/recon-1.06-r2.ebuild
new file mode 100644
index 000000000000..12a9207c9f42
--- /dev/null
+++ b/sci-biology/recon/recon-1.06-r2.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="4"
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
+HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
+SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="examples"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/RECON${PV}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${PV}-buffer-overflow.patch \
+ "${FILESDIR}"/${P}-respect.patch
+ sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
+ tc-export CC
+}
+
+src_compile() {
+ emake -C src
+}
+
+src_install() {
+ dobin scripts/*
+ exeinto /usr/libexec/${PN}
+ doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
+ dodoc 00README
+ insinto /usr/share/${PN}
+ use examples && doins -r Demos
+}
diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest
new file mode 100644
index 000000000000..599aa33f9dd1
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/Manifest
@@ -0,0 +1 @@
+DIST repeatmaskerlibraries-20120418.tar.gz 28059668 SHA256 7bd44a70ee33ef60ab829b4cb84a2a82a6fa923e2992071f374b7a473e4dac62 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 WHIRLPOOL 1da932f84c591221c61177116d734d00c36c52d588bcdab73ed63e8128b9c90a63f855bf4e8e603167e059f98465460b5b2e7e00e4a724bec230d27b1b32a31a
diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild
new file mode 100644
index 000000000000..4c6b6b6ba01e
--- /dev/null
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="A special version of RepBase used by RepeatMasker"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="repeatmaskerlibraries-${PV}.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/Libraries"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+ einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz"
+ einfo 'at http://www.girinst.org/'
+ einfo '(select the "Repbase Update - RepeatMasker edition" link)'
+ einfo 'and place it in '${DISTDIR}
+}
+
+src_install() {
+ insinto /usr/share/repeatmasker/Libraries
+ doins "${S}"/RepeatMaskerLib.embl
+ dodoc README
+ dohtml README.html
+}
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
new file mode 100644
index 000000000000..5f4296e01d47
--- /dev/null
+++ b/sci-biology/repeatmasker/Manifest
@@ -0,0 +1 @@
+DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
new file mode 100644
index 000000000000..acef7d5caf4b
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PV=${PV//\./-}
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+ sci-biology/rmblast
+ sci-biology/trf
+ sci-biology/repeatmasker-libraries"
+
+S="${WORKDIR}/RepeatMasker"
+
+src_configure() {
+ sed -i -e 's/system( "clear" );//' \
+ -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
+ echo "
+env
+/usr/share/${PN}
+/usr/bin
+2
+/opt/rmblast/bin
+Y
+5" | "${S}/configure" || die "configure failed"
+ sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
+ -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
+ -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
+ "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+ exeinto /usr/share/${PN}
+ for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+ doexe $i || die
+ dosym /usr/share/${PN}/$i /usr/bin/$i || die
+ done
+
+ dodir /usr/share/${PN}/lib
+ insinto /usr/share/${PN}/lib
+ doins "${S}"/*.pm || die
+
+ insinto /usr/share/${PN}
+ doins -r util Matrices Libraries taxonomy.dat *.help || die
+ keepdir /usr/share/${PN}/Libraries
+
+ dodoc README INSTALL *.help
+}
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
new file mode 100644
index 000000000000..00c455fce326
--- /dev/null
+++ b/sci-biology/rmblast/Manifest
@@ -0,0 +1 @@
+DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a
diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
new file mode 100644
index 000000000000..70200d59ea4a
--- /dev/null
+++ b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
@@ -0,0 +1,865 @@
+ c++/include/corelib/ncbiexpt.hpp | 4 +-
+ c++/include/corelib/ncbimisc.hpp | 2 +
+ c++/include/corelib/ncbiobj.hpp | 2 +-
+ c++/include/corelib/ncbistl.hpp | 6 +-
+ c++/include/corelib/ncbistr.hpp | 2 +-
+ c++/include/corelib/test_boost.hpp | 44 +++++-
+ c++/include/dbapi/driver/dbapi_object_convert.hpp | 8 +-
+ .../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +-
+ c++/include/serial/impl/stltypes.hpp | 16 ++-
+ c++/include/serial/iterator.hpp | 6 +-
+ c++/include/serial/serialbase.hpp | 8 +-
+ c++/include/util/bitset/bmfunc.h | 7 +
+ c++/include/util/linkedset.hpp | 16 +--
+ c++/include/util/rangemap.hpp | 4 +-
+ c++/src/connect/ncbi_gnutls.c | 19 ++-
+ c++/src/corelib/ncbifile.cpp | 2 +-
+ c++/src/corelib/test_boost.cpp | 156 ++++++++++++++++++++-
+ c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +-
+ c++/src/serial/stdtypes.cpp | 8 +-
+ 19 files changed, 269 insertions(+), 45 deletions(-)
+
+diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp
+index a9cf850..6d90e74 100644
+--- a/c++/include/corelib/ncbiexpt.hpp
++++ b/c++/include/corelib/ncbiexpt.hpp
+@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from)
+ exception_class(const exception_class& other) \
+ : base_class(other) \
+ { \
+- x_Assign(other); \
++ this->x_Assign(other); \
+ } \
+ public: \
+ virtual ~exception_class(void) throw() {} \
+@@ -1154,7 +1154,7 @@ public:
+ : TBase( other)
+ {
+ m_Errno = other.m_Errno;
+- x_Assign(other);
++ this->x_Assign(other);
+ }
+
+ /// Destructor.
+diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp
+index f45d280..f0c030d 100644
+--- a/c++/include/corelib/ncbimisc.hpp
++++ b/c++/include/corelib/ncbimisc.hpp
+@@ -57,6 +57,8 @@
+ * @{
+ */
+
++#include <stdlib.h>
++
+ #ifndef NCBI_ESWITCH_DEFINED
+ #define NCBI_ESWITCH_DEFINED
+
+diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp
+index 4f83db4..815c188 100644
+--- a/c++/include/corelib/ncbiobj.hpp
++++ b/c++/include/corelib/ncbiobj.hpp
+@@ -2128,7 +2128,7 @@ public:
+ CIRef<Interface, TThisType> ref(
+ dynamic_cast<Interface*>(proxy->GetLockedObject()), *this);
+ if (ref.NotNull()) {
+- Unlock(ref.GetPointer());
++ this->Unlock(ref.GetPointer());
+ }
+ return ref;
+ }
+diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp
+index 0bf465a..0618d9d 100644
+--- a/c++/include/corelib/ncbistl.hpp
++++ b/c++/include/corelib/ncbistl.hpp
+@@ -37,7 +37,6 @@
+
+ #include <common/ncbi_export.h>
+
+-
+ // Get rid of some warnings in MSVC++ 6.00
+ #if (_MSC_VER >= 1200)
+ // too long identificator name in the debug info; truncated
+@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName)
+ #endif
+
+ #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP)
++# if defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400
++# include <algorithm>
++# endif
+ // This template is used by some stl algorithms (sort, reverse...)
+ // We need to have our own implementation because some C++ Compiler vendors
+ // implemented it by using a temporary variable and an assignment operator
+@@ -174,7 +176,7 @@ template<typename Iter>
+ inline
+ void iter_swap( Iter it1, Iter it2 )
+ {
+- swap( *it1, * it2 );
++ swap( *it1, *it2 );
+ }
+
+ END_STD_SCOPE
+diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp
+index db7054f..63e3299 100644
+--- a/c++/include/corelib/ncbistr.hpp
++++ b/c++/include/corelib/ncbistr.hpp
+@@ -2583,7 +2583,7 @@ public:
+ : TBase(other)
+ {
+ m_Pos = other.m_Pos;
+- x_Assign(other);
++ this->x_Assign(other);
+ }
+
+ /// Destructor.
+diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp
+index 69c41f3..4cd77d3 100644
+--- a/c++/include/corelib/test_boost.hpp
++++ b/c++/include/corelib/test_boost.hpp
+@@ -56,10 +56,18 @@
+ # undef BOOST_AUTO_TEST_MAIN
+ #endif
+
++#ifdef NCBI_COMPILER_MSVC
++# pragma warning(push)
++// 'class' : class has virtual functions, but destructor is not virtual
++# pragma warning(disable: 4265)
++#endif
++
++#include <boost/version.hpp>
+ #include <boost/test/auto_unit_test.hpp>
+ #include <boost/test/floating_point_comparison.hpp>
+ #include <boost/test/framework.hpp>
+ #include <boost/test/execution_monitor.hpp>
++#include <boost/test/parameterized_test.hpp>
+
+ #include <boost/preprocessor/tuple/rem.hpp>
+ #include <boost/preprocessor/repeat.hpp>
+@@ -72,6 +80,7 @@
+ #undef BOOST_CHECK_THROW_IMPL
+ #undef BOOST_CHECK_NO_THROW_IMPL
+ #undef BOOST_FIXTURE_TEST_CASE
++#undef BOOST_PARAM_TEST_CASE
+
+ #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL ) \
+ try { \
+@@ -109,6 +118,12 @@ catch( ... ) { \
+ } \
+ /**/
+
++#if BOOST_VERSION >= 104200
++# define NCBI_BOOST_LOCATION() , boost::execution_exception::location()
++#else
++# define NCBI_BOOST_LOCATION()
++#endif
++
+ #define BOOST_FIXTURE_TEST_CASE( test_name, F ) \
+ struct test_name : public F { void test_method(); }; \
+ \
+@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )() \
+ ::framework::current_test_case().p_name \
+ << "\"" << ex); \
+ throw boost::execution_exception( \
+- boost::execution_exception::cpp_exception_error, ""); \
++ boost::execution_exception::cpp_exception_error, "" \
++ NCBI_BOOST_LOCATION() ); \
+ } \
+ } \
+ \
+@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \
+ void test_name::test_method() \
+ /**/
+
++#define BOOST_PARAM_TEST_CASE( function, begin, end ) \
++ ::NCBI_NS_NCBI::NcbiTestGenTestCases( function, \
++ BOOST_TEST_STRINGIZE( function ), \
++ (begin), (end) ) \
++/**/
++
+ /// Set timeout value for the test case created using auto-registration
+ /// facility.
+ #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n) \
+@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \
+ } BOOST_JOIN( test_name, _timeout_spec_inst ); \
+ /**/
+
++/// Automatic registration of the set of test cases based on some function
++/// accepting one parameter. Set of parameters used to call that function is
++/// taken from iterator 'begin' which is incremented until it reaches 'end'.
++///
++/// @sa BOOST_PARAM_TEST_CASE
++#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end ) \
++ BOOST_AUTO_TU_REGISTRAR(function) ( \
++ BOOST_PARAM_TEST_CASE(function, begin, end)) \
++/**/
++
++#define BOOST_TIMEOUT(M) \
++ do { \
++ static string s(M); \
++ throw boost::execution_exception( \
++ boost::execution_exception::timeout_error, s \
++ NCBI_BOOST_LOCATION()); \
++ } while (0) \
++/**/
++
++
+
+ #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT) \
+ BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL)
+diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp
+index 6fcde61..eddde81 100644
+--- a/c++/include/dbapi/driver/dbapi_object_convert.hpp
++++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp
+@@ -67,7 +67,7 @@ public:
+ operator const CTime&(void) const;
+
+ private:
+- mutable obj_type& m_Value;
++ obj_type& m_Value;
+ };
+
+ ////////////////////////////////////////////////////////////////////////////////
+@@ -92,7 +92,7 @@ public:
+ operator const CTime&(void) const;
+
+ private:
+- mutable obj_type& m_Value;
++ obj_type& m_Value;
+ };
+
+ ////////////////////////////////////////////////////////////////////////////////
+@@ -133,7 +133,7 @@ public:
+ operator const CTime&(void) const;
+
+ private:
+- mutable obj_type& m_Value;
++ obj_type& m_Value;
+ };
+
+ ////////////////////////////////////////////////////////////////////////////////
+@@ -174,7 +174,7 @@ public:
+ operator const CTime&(void) const;
+
+ private:
+- mutable obj_type& m_Value;
++ obj_type& m_Value;
+ };
+
+ ////////////////////////////////////////////////////////////////////////////////
+diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
+index 0792a6d..b6bd64b 100644
+--- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
++++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
+@@ -231,7 +231,7 @@ protected:
+
+ private:
+ const string& m_SPName;
+- mutable impl::CConnection& m_Conn;
++ impl::CConnection& m_Conn;
+ };
+
+
+diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp
+index d41ab94..7d9e3ce 100644
+--- a/c++/include/serial/impl/stltypes.hpp
++++ b/c++/include/serial/impl/stltypes.hpp
+@@ -412,6 +412,7 @@ public:
+ typedef StlIterator TStlIterator;
+ typedef TypeInfoIterator TTypeInfoIterator;
+ typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
++ typedef CStlClassInfoFunctions<Container> CParent;
+
+ static TStlIterator& It(TTypeInfoIterator& iter)
+ {
+@@ -437,7 +438,8 @@ public:
+ }
+ static bool InitIterator(TTypeInfoIterator& iter)
+ {
+- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
++ TStlIterator stl_iter
++ = CParent::Get(iter.GetContainerPtr()).begin();
+ if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
+ void* data = &iter.m_IteratorData;
+ new (data) TStlIterator(stl_iter);
+@@ -445,7 +447,7 @@ public:
+ else {
+ iter.m_IteratorData = new TStlIterator(stl_iter);
+ }
+- return stl_iter != Get(iter.GetContainerPtr()).end();
++ return stl_iter != CParent::Get(iter.GetContainerPtr()).end();
+ }
+ static void ReleaseIterator(TTypeInfoIterator& iter)
+ {
+@@ -466,7 +468,7 @@ public:
+
+ static bool NextElement(TTypeInfoIterator& iter)
+ {
+- return ++It(iter) != Get(iter.GetContainerPtr()).end();
++ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end();
+ }
+ static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
+ {
+@@ -503,7 +505,7 @@ public:
+
+ static bool EraseElement(TTypeInfoIterator& iter)
+ {
+- TStlIterator& it = It(iter);
++ TStlIterator& it = CParent::It(iter);
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+ it = c->erase(it);
+ return it != c->end();
+@@ -511,7 +513,7 @@ public:
+ static void EraseAllElements(TTypeInfoIterator& iter)
+ {
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+- c->erase(It(iter), c->end());
++ c->erase(CParent::It(iter), c->end());
+ }
+
+ static void SetIteratorFunctions(CStlOneArgTemplate* info)
+@@ -542,7 +544,7 @@ public:
+ }
+ static bool EraseElement(TTypeInfoIterator& iter)
+ {
+- TStlIterator& it = It(iter);
++ TStlIterator& it = CParent::It(iter);
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+ TStlIterator erase = it++;
+ c->erase(erase);
+@@ -551,7 +553,7 @@ public:
+ static void EraseAllElements(TTypeInfoIterator& iter)
+ {
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+- c->erase(It(iter), c->end());
++ c->erase(CParent::It(iter), c->end());
+ }
+
+ static void SetIteratorFunctions(CStlOneArgTemplate* info)
+diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp
+index 25e1193..cddb046 100644
+--- a/c++/include/serial/iterator.hpp
++++ b/c++/include/serial/iterator.hpp
+@@ -491,13 +491,13 @@ protected:
+ CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo)
+ : m_NeedType(needType)
+ {
+- Init(beginInfo);
++ this->Init(beginInfo);
+ }
+ CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo,
+ const string& filter)
+ : m_NeedType(needType)
+ {
+- Init(beginInfo, filter);
++ this->Init(beginInfo, filter);
+ }
+
+ virtual bool CanSelect(const CConstObjectInfo& object)
+@@ -599,7 +599,7 @@ public:
+
+ CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo)
+ {
+- Init(beginInfo);
++ this->Init(beginInfo);
+ return *this;
+ }
+
+diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp
+index be6a4f9..d59fb25 100644
+--- a/c++/include/serial/serialbase.hpp
++++ b/c++/include/serial/serialbase.hpp
+@@ -364,11 +364,15 @@ public:
+ // cast to object type
+ TObject& operator*(void)
+ {
+- return *reinterpret_cast<TObject*>(m_Buffer);
++ TObject* ptr = static_cast<TObject*>
++ (static_cast<void*>(m_Buffer));
++ return *ptr;
+ }
+ const TObject& operator*(void) const
+ {
+- return *reinterpret_cast<const TObject*>(m_Buffer);
++ const TObject* ptr = static_cast<const TObject*>
++ (static_cast<const void*>(m_Buffer));
++ return *ptr;
+ }
+
+ // construct/destruct object
+diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h
+index 5917ee5..a8c204b 100644
+--- a/c++/include/util/bitset/bmfunc.h
++++ b/c++/include/util/bitset/bmfunc.h
+@@ -37,6 +37,13 @@ For more information please visit: http://bmagic.sourceforge.net
+ namespace bm
+ {
+
++bm::id_t bit_block_any_range(const bm::word_t* block,
++ bm::word_t left,
++ bm::word_t right);
++
++bm::id_t bit_block_calc_count_range(const bm::word_t* block,
++ bm::word_t left,
++ bm::word_t right);
+
+ /*!
+ @brief Structure with statistical information about bitset's memory
+diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp
+index e8bbe6e..364164b 100644
+--- a/c++/include/util/linkedset.hpp
++++ b/c++/include/util/linkedset.hpp
+@@ -268,10 +268,10 @@ public:
+ pair<iterator, bool> ins = m_Container.insert(value);
+ if ( ins.second ) {
+ if ( ins.first == begin() )
+- insertToStart(*ins.first);
++ this->insertToStart(*ins.first);
+ else {
+ iterator prev = ins.first;
+- insertAfter(*--prev, *ins.first);
++ this->insertAfter(*--prev, *ins.first);
+ }
+ }
+ return ins;
+@@ -280,10 +280,10 @@ public:
+ void erase(iterator iter)
+ {
+ if ( iter == begin() )
+- removeFromStart(*iter);
++ this->removeFromStart(*iter);
+ else {
+ iterator prev = iter;
+- removeAfter(*--prev, *iter);
++ this->removeAfter(*--prev, *iter);
+ }
+ m_Container.erase(iter);
+ }
+@@ -422,10 +422,10 @@ public:
+ {
+ iterator iter = m_Container.insert(value);
+ if ( iter == begin() )
+- insertToStart(get(iter));
++ this->insertToStart(get(iter));
+ else {
+ iterator prev = iter;
+- insertAfter(get(--prev), get(iter));
++ this->insertAfter(get(--prev), get(iter));
+ }
+ return iter;
+ }
+@@ -433,10 +433,10 @@ public:
+ void erase(iterator iter)
+ {
+ if ( iter == begin() )
+- removeFromStart(get(iter));
++ this->removeFromStart(get(iter));
+ else {
+ iterator prev = iter;
+- removeAfter(get(--prev), get(iter));
++ this->removeAfter(get(--prev), get(iter));
+ }
+ m_Container.erase(iter);
+ }
+diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp
+index c4f5f37..56e267d 100644
+--- a/c++/include/util/rangemap.hpp
++++ b/c++/include/util/rangemap.hpp
+@@ -578,7 +578,7 @@ public:
+ // get level
+
+ // insert element
+- TSelectMapI selectIter = insertLevel(selectKey);
++ TSelectMapI selectIter = this->insertLevel(selectKey);
+ pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value);
+
+ pair<iterator, bool> ret;
+@@ -640,7 +640,7 @@ public:
+ // insert element
+ iterator ret;
+ ret.m_Range = range_type::GetWhole();
+- ret.m_SelectIter = insertLevel(selectKey);
++ ret.m_SelectIter = this->insertLevel(selectKey);
+ ret.m_SelectIterEnd = this->m_SelectMap.end();
+ ret.m_LevelIter = ret.m_SelectIter->second.insert(value);
+ return ret;
+diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c
+index f0242b7..8b13713 100644
+--- a/c++/src/connect/ncbi_gnutls.c
++++ b/c++/src/connect/ncbi_gnutls.c
+@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = {
+ 0
+ };
+ static const int kGnuTlsCompPrio[] = {
+- GNUTLS_COMP_LZO,
+ GNUTLS_COMP_ZLIB,
+ GNUTLS_COMP_NULL,
+ 0
+@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error)
+ }
+
+
++/*ARGSUSED*/
++static void x_set_errno(gnutls_session_t session, int error)
++{
++# ifdef LIBGNUTLS_VERSION_NUMBER
++# if \
++ LIBGNUTLS_VERSION_MAJOR > 1 || \
++ LIBGNUTLS_VERSION_MINOR > 5 || \
++ LIBGNUTLS_VERSION_PATCH > 3
++ gnutls_transport_set_errno(session, error);
++ return;
++# endif /*LIBGNUTLS_VERSION >= 1.5.4*/
++# endif /*LIBGNUTLS_VERSION_NUMBER*/
++ /*NOTREACHED*/
++ if (error)
++ errno = error;
++}
++
++
+ static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr,
+ void* buf, size_t size)
+ {
+diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp
+index d751e62..fdc81c7 100644
+--- a/c++/src/corelib/ncbifile.cpp
++++ b/c++/src/corelib/ncbifile.cpp
+@@ -51,8 +51,8 @@
+ # include <dirent.h>
+ # include <pwd.h>
+ # include <fcntl.h>
+-# include <sys/time.h>
+ # include <sys/mman.h>
++# include <sys/time.h>
+ # ifdef HAVE_SYS_STATVFS_H
+ # include <sys/statvfs.h>
+ # endif
+diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp
+index dfd9cc8..f93d2ca 100644
+--- a/c++/src/corelib/test_boost.cpp
++++ b/c++/src/corelib/test_boost.cpp
+@@ -41,6 +41,7 @@
+ #ifndef BOOST_TEST_NO_LIB
+ # define BOOST_TEST_NO_LIB
+ #endif
++#define BOOST_TEST_NO_MAIN
+ #include <corelib/test_boost.hpp>
+
+ #include <boost/preprocessor/cat.hpp>
+@@ -95,6 +96,7 @@ const char* kTestResultTimeout = "timeout";
+ const char* kTestResultAborted = "aborted";
+ const char* kTestResultSkipped = "skipped";
+ const char* kTestResultDisabled = "disabled";
++const char* kTestResultToFix = "tofix";
+
+
+ typedef but::results_reporter::format TBoostRepFormatter;
+@@ -168,14 +170,24 @@ public:
+ unsigned long elapsed);
+ virtual
+ void test_unit_skipped(ostream& ostr, but::test_unit const& tu);
++#if BOOST_VERSION >= 104200
++ virtual
++ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd,
++ boost::execution_exception const& ex);
++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
++ using TBoostLogFormatter::log_exception;
++#else
+ virtual
+ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd,
+ but::const_string explanation);
++#endif
+ virtual
+ void log_entry_start (ostream& ostr, but::log_entry_data const& led,
+ log_entry_types let);
+ virtual
+ void log_entry_value (ostream& ostr, but::const_string value);
++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
++ using TBoostLogFormatter::log_entry_value;
+ virtual
+ void log_entry_finish (ostream& ostr);
+
+@@ -402,10 +414,15 @@ public:
+
+ /// Mark test case as failed due to hit of the timeout
+ void SetTestTimedOut(but::test_case* tc);
++ /// Register the fact of test failure
++ void SetTestErrored(but::test_case* tc);
++ /// Check if given test is marked as requiring fixing in the future
++ bool IsTestToFix(const but::test_unit* tu);
+
+ /// Get number of actually executed tests
+ int GetRanTestsCount(void);
+-
++ /// Get number of tests that were failed but are marked to be fixed
++ int GetToFixTestsCount(void);
+ /// Get string representation of result of test execution
+ string GetTestResultString(but::test_unit* tu);
+
+@@ -415,6 +432,11 @@ public:
+ /// Check if user initialization functions failed
+ bool IsInitFailed(void);
+
++ /// Check if there were any test errors
++ bool HasTestErrors(void);
++ /// Check if there were any timeouted tests
++ bool HasTestTimeouts(void);
++
+ private:
+ typedef list<TNcbiTestUserFunction> TUserFuncsList;
+
+@@ -493,6 +515,8 @@ private:
+ TUnitsSet m_DisabledTests;
+ /// List of all tests which result is a timeout
+ TUnitsSet m_TimedOutTests;
++ /// List of all tests marked as in need of fixing in the future
++ TUnitsSet m_ToFixTests;
+ /// List of all dependencies for each test having dependencies
+ TUnitToManyMap m_TestDeps;
+ /// Observer to make test dependencies and look for unit's timeouts
+@@ -512,12 +536,18 @@ private:
+ /// String representation for whole test timeout (real value taken from
+ /// CHECK_TIMEOUT in Makefile).
+ string m_TimeoutStr;
++ /// Multiplicator for timeouts
++ double m_TimeMult;
+ /// Timer measuring elapsed time for the whole test
+ CStopWatch m_Timer;
+ /// Timeout that was set in currently executing unit before adjustment
+ ///
+ /// @sa AdjustTestTimeout()
+ unsigned int m_CurUnitTimeout;
++ /// Flag showing if there were some test errors
++ bool m_HasTestErrors;
++ /// Flag showing if there were some timeouted tests
++ bool m_HasTestTimeouts;
+ };
+
+
+@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void)
+ m_RunMode (0),
+ m_DummyTest(NULL),
+ m_Timeout (0),
+- m_Timer (CStopWatch::eStart)
++ m_TimeMult (1),
++ m_Timer (CStopWatch::eStart),
++ m_HasTestErrors(false),
++ m_HasTestTimeouts(false)
+ {
+ m_Reporter = new CNcbiBoostReporter();
+ m_Logger = new CNcbiBoostLogger();
+@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void)
+ return result;
+ }
+
++int
++CNcbiTestApplication::GetToFixTestsCount(void)
++{
++ int result = 0;
++ ITERATE(TUnitsSet, it, m_ToFixTests) {
++ if (!but::results_collector.results((*it)->p_id).passed())
++ ++result;
++ }
++ return result;
++}
++
++inline bool
++CNcbiTestApplication::IsTestToFix(const but::test_unit* tu)
++{
++ return m_ToFixTests.find(const_cast<but::test_unit*>(tu))
++ != m_ToFixTests.end();
++}
++
+ inline void
+ CNcbiTestApplication::x_SetupBoostReporters(void)
+ {
+@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[])
+ return NULL;
+ }
+
++inline bool
++CNcbiTestApplication::HasTestErrors(void)
++{
++ return m_HasTestErrors;
++}
++
++inline bool
++CNcbiTestApplication::HasTestTimeouts(void)
++{
++ return m_HasTestTimeouts;
++}
++
+ void
+ CNcbiTestsCollector::visit(but::test_case const& test)
+ {
+@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu,
+ // elapsed comes in microseconds
+ if (timeout != 0 && timeout < elapsed / 1000000) {
+ boost::execution_exception ex(
+- boost::execution_exception::timeout_error, "Timeout exceeded");
++ boost::execution_exception::timeout_error, "Timeout exceeded"
++ NCBI_BOOST_LOCATION());
+ but::framework::exception_caught(ex);
+ }
++
++ but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id];
++ if (!tr.passed() && s_GetTestApp().IsTestToFix(&tu)) {
++ static_cast<but::readwrite_property<bool>& >(
++ static_cast<but::class_property<bool>& >(
++ tr.p_skipped)).set(true);
++ static_cast<but::readwrite_property<but::counter_t>& >(
++ static_cast<but::class_property<but::counter_t>& >(
++ tr.p_assertions_failed)).set(0);
++ }
+ }
+
+ void
+@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu)
+ m_Upper->test_unit_skipped(ostr, tu);
+ }
+
++#if BOOST_VERSION >= 104200
++void
++CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
++ boost::execution_exception const& ex)
++{
++ m_Upper->log_exception(ostr, lcd, ex);
++}
++#else
+ void
+ CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
+ but::const_string explanation)
+ {
+ m_Upper->log_exception(ostr, lcd, explanation);
+ }
++#endif
+
+ void
+ CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led,
+@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name)
+ END_NCBI_SCOPE
+
+
++using namespace but;
++
+ /// Global initialization function called from Boost framework
+-but::test_suite*
++test_suite*
+ init_unit_test_suite(int argc, char* argv[])
+ {
+ return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv);
+ }
++
++// This main() is mostly a copy from Boost's unit_test_main.ipp
++int
++main(int argc, char* argv[])
++{
++ int result = boost::exit_success;
++
++ try {
++ framework::init( &init_unit_test_suite, argc, argv );
++
++ if( !runtime_config::test_to_run().is_empty() ) {
++ test_case_filter filter( runtime_config::test_to_run() );
++
++ traverse_test_tree( framework::master_test_suite().p_id, filter );
++ }
++
++ framework::run();
++
++ // Let's try to make report in case of any error after all catches.
++ //results_reporter::make_report();
++
++ if (!runtime_config::no_result_code()) {
++ result = results_collector.results( framework::master_test_suite().p_id ).result_code();
++ if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors()
++ && NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts())
++ {
++ // This should certainly go to the output. So we can use only
++ // printf, nothing else.
++ printf("There were no test failures, only timeouts.\n"
++ " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n");
++ }
++ }
++ }
++#if BOOST_VERSION >= 104200
++ catch( framework::nothing_to_test const& ) {
++ result = boost::exit_success;
++ }
++#endif
++ catch( framework::internal_error const& ex ) {
++ results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl;
++
++ result = boost::exit_exception_failure;
++ }
++ catch( framework::setup_error const& ex ) {
++ results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl;
++
++ result = boost::exit_exception_failure;
++ }
++ catch( std::exception const& ex ) {
++ results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl;
++
++ result = boost::exit_exception_failure;
++ }
++ catch( ... ) {
++ results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl;
++
++ result = boost::exit_exception_failure;
++ }
++
++ results_reporter::make_report();
++
++ return result;
++}
+diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
+index 92e817f..cfab8ab 100644
+--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
++++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
+@@ -1199,7 +1199,7 @@ private:
+ CSeqDBAtlasHolder m_AtlasHolder;
+
+ /// Reference to memory management layer.
+- mutable CSeqDBAtlas & m_Atlas;
++ CSeqDBAtlas & m_Atlas;
+
+ /// The list of database names provided to the constructor.
+ string m_DBNames;
+diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp
+index f6fa651..d6e8f80 100644
+--- a/c++/src/serial/stdtypes.cpp
++++ b/c++/src/serial/stdtypes.cpp
+@@ -720,7 +720,7 @@ public:
+ if ( IsSigned() ) {
+ // signed -> unsigned
+ // check for negative value
+- if ( IsNegative(value) )
++ if ( CParent::IsNegative(value) )
+ ThrowIntegerOverflow();
+ }
+ if ( sizeof(value) > sizeof(result) ) {
+@@ -751,7 +751,7 @@ public:
+ // unsigned -> signed
+ if ( sizeof(value) == sizeof(result) ) {
+ // same size - check for sign change only
+- if ( IsNegative(result) )
++ if ( CParent::IsNegative(result) )
+ ThrowIntegerOverflow();
+ }
+ }
+@@ -786,7 +786,7 @@ public:
+ if ( IsSigned() ) {
+ // signed -> unsigned
+ // check for negative value
+- if ( IsNegative(value) )
++ if ( CParent::IsNegative(value) )
+ ThrowIntegerOverflow();
+ }
+ if ( sizeof(value) > sizeof(result) ) {
+@@ -817,7 +817,7 @@ public:
+ // unsigned -> signed
+ if ( sizeof(value) == sizeof(result) ) {
+ // same size - check for sign change only
+- if ( IsNegative(result) )
++ if ( CParent::IsNegative(result) )
+ ThrowIntegerOverflow();
+ }
+ }
diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/rmblast/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
new file mode 100644
index 000000000000..768b309813bc
--- /dev/null
+++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_NCBI_BLAST_V=2.2.23+
+
+DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+"
+HOMEPAGE="http://www.repeatmasker.org/RMBlast.html"
+SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-libs/boost"
+DEPEND="${RDEPEND}
+ app-arch/cpio"
+
+S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++"
+
+src_prepare() {
+ filter-ldflags -Wl,--as-needed
+ sed \
+ -e 's/-print-file-name=libstdc++.a//' \
+ -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+ -e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \
+ -i src/build-system/configure || die
+ epatch "${FILESDIR}"/${P}-gcc47.patch
+}
+
+src_configure() {
+ tc-export CXX CC
+
+ "${S}"/configure --without-debug \
+ --with-mt \
+ --without-static \
+ --with-dll \
+ --prefix="${ED}"/opt/${PN} \
+ --with-boost="${EPREFIX}/usr/include/boost" \
+ || die
+}
diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest
new file mode 100644
index 000000000000..f56b09e2659c
--- /dev/null
+++ b/sci-biology/rnaview/Manifest
@@ -0,0 +1 @@
+DIST rnaview-20040713.tar.bz2 433916 SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17 SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e WHIRLPOOL 7ae8953a8028da0eb525a6b33964267b15721dbe148f5077cf2c7e47c7cc2e3a47616bcc944e7f8180c0696c27ac16c53bd3847d02db5a575df3cebba29dd169
diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
new file mode 100644
index 000000000000..009f6e79ae86
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch
@@ -0,0 +1,13 @@
+Fix implicit function declaration
+
+--- src/xml2ps.c
++++ src/xml2ps.c
+@@ -36,7 +36,7 @@
+ void read_sugar_syn(char *inpfile, long **sugar_syn);
+ void get_sugar_syn(FILE *inp, char *value_ch);
+ void get_chain_broken(long nres, double **a, double **b, long *chain_broken);
+-
++extern void get_BDIR(char *BDIR, char *filename);
+
+
+ FILE *psfile;
diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
new file mode 100644
index 000000000000..1af72f581fbf
--- /dev/null
+++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
@@ -0,0 +1,87 @@
+ Makefile | 20 +++++++++++++++++---
+ rnaml2ps/Makefile | 19 ++++++++++++-------
+ 2 files changed, 29 insertions(+), 10 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 452e6c4..00d35f0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,4 @@
+-CC = cc
++CC ?= cc
+
+
+
+@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \
+ $(OBJ)/multiple.o \
+ $(OBJ)/statistics.o
+
++.PHONY: clean all install
++
++SUBDIRS = rnaml2ps
++
+ all: $(RNAVIEW)
++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done
+
+-CFLAGS = $(LINCLUDES)
++CFLAGS += $(LINCLUDES)
+
+ $(RNAVIEW) : $(HFILES) $(OBJ_FILE)
+- $(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB)
+
+
+
+@@ -111,6 +116,15 @@ $(OBJ)/statistics.o : $(SRC)/statistics.c
+ clean:
+ @rm -f $(OBJ)/*.o
+ @rm -f $(ALLTARGETS)
++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done
++
++install:
++ install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview
++ mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS
++ install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS
++ mkdir -p $(DESTDIR)/usr/share/rnaview/test
++ install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test
++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done
+
+ export:
+ mkdir -p $(EXPORT_DIR)
+diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile
+index d207655..2278ccc 100644
+--- a/rnaml2ps/Makefile
++++ b/rnaml2ps/Makefile
+@@ -1,20 +1,25 @@
+-CFLAGS = -O
+-CC = cc
++CFLAGS ?= -O
++CC ?= cc
+
+ # ++++++++++++++++++++++++++++ Program RNADRAW
+ RNADRAW = rnaml2ps
+ OBJS_RNADRAW = rnaml2ps.o nrutil.o
+
++all: $(RNADRAW)
++
+ $(RNADRAW): $(OBJS_RNADRAW)
+- $(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
++ $(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
+
+ nrutil.o : nrutil.c
+- cc -c nrutil.c
++ $(CC) $(CFLAGS) -c nrutil.c
+
+ rnaml2ps.o : rnaml2ps.c
+- cc -c rnaml2ps.c
++ $(CC) $(CFLAGS) -c rnaml2ps.c
+
+
+-.PHONY : clean
++.PHONY : clean all install
+ clean:
+- rm *.o
++ rm -f *.o
++
++install:
++ install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW)
diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml
new file mode 100644
index 000000000000..b243b0c8da63
--- /dev/null
+++ b/sci-biology/rnaview/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ The RNAView program generates 2-dimensional displays of RNA/DNA
+ secondary structures with tertiary interactions. RNAView
+ automatically identifies and classifies the types of base pairs that
+ are formed in nucleic acid structures, fully implementing Leontis and
+ Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge
+ hydrogen bonding interactions.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/rnaview/rnaview-20040713-r2.ebuild b/sci-biology/rnaview/rnaview-20040713-r2.ebuild
new file mode 100644
index 000000000000..ac9168c57512
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713-r2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-makefile.patch \
+ "${FILESDIR}"/${P}-implicit.patch
+ cat <<- EOF > 22rnaview
+ RNAVIEW="/usr/share/${PN}"
+ EOF
+}
+
+src_compile() {
+ emake CC="$(tc-getCC)" || die
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die
+ dodoc README || die
+ doenvd 22rnaview || die
+}
diff --git a/sci-biology/rnaview/rnaview-20040713-r3.ebuild b/sci-biology/rnaview/rnaview-20040713-r3.ebuild
new file mode 100644
index 000000000000..5f46e6bc586c
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713-r3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-makefile.patch \
+ "${FILESDIR}"/${P}-implicit.patch
+ cat <<- EOF > 22rnaview
+ RNAVIEW="${EPREFIX}/usr/share/${PN}"
+ EOF
+ tc-export CC
+}
+
+src_install() {
+ default
+ doenvd 22rnaview
+}
diff --git a/sci-biology/rnaview/rnaview-20040713.ebuild b/sci-biology/rnaview/rnaview-20040713.ebuild
new file mode 100644
index 000000000000..9bbb7a81f3cf
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~amd64 x86"
+IUSE=""
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ sed -e "s/CC = cc/CC = $(tc-getCC)/" \
+ -e "s/CFLAGS =/CFLAGS = ${CFLAGS}/" \
+ -i Makefile || die
+}
+
+src_compile() {
+ make clean
+ make || die
+ cd "${S}"/rnaml2ps
+ make clean
+ make || die
+ cd "${S}"/test
+ rm '.#t'
+}
+
+src_install() {
+ dobin bin/rnaview rnaml2ps/rnaml2ps || die
+ dodoc README || die
+ mkdir -p "${D}"/usr/share/${PN}
+ cp -r BASEPARS test "${D}"/usr/share/${PN}
+}
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
new file mode 100644
index 000000000000..8178b5d5369f
--- /dev/null
+++ b/sci-biology/samtools/Manifest
@@ -0,0 +1,5 @@
+DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac
+DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5
+DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832
+DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449
+DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4
diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
new file mode 100644
index 000000000000..d5ff3bd45da5
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
@@ -0,0 +1,183 @@
+ Makefile | 22 +++++++++++-----------
+ bcftools/Makefile | 12 ++++++------
+ misc/Makefile | 28 ++++++++++++++--------------
+ 3 files changed, 31 insertions(+), 31 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 2f51bfc..4dda5a4 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+-CC= gcc
+-CFLAGS= -g -Wall -O2
+-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
+-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
++CC?= gcc
++CFLAGS?= -g -Wall -O2
++#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib
++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
+ KNETFILE_O= knetfile.o
+ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses
+ .PHONY: all lib
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+@@ -44,16 +44,16 @@ libbam.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+ samtools:lib-recur $(AOBJS)
+- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
+
+ razip:razip.o razf.o $(KNETFILE_O)
+- $(CC) $(CFLAGS) -o $@ $^ -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz
+
+ bgzip:bgzip.o bgzf.o $(KNETFILE_O)
+- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread
+
+ bgzf.o:bgzf.c bgzf.h
+- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
+
+ razip.o:razf.h
+ bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
+@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS)
+ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
+
+ libbam.so.1-local:$(LOBJS)
+- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread
+
+ dylib:
+ @$(MAKE) cleanlocal; \
+diff --git a/bcftools/Makefile b/bcftools/Makefile
+index be831de..7ef796c 100644
+--- a/bcftools/Makefile
++++ b/bcftools/Makefile
+@@ -1,6 +1,6 @@
+-CC= gcc
+-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
+-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
++CC?= gcc
++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+ OMISC= ..
+ AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
+@@ -11,14 +11,14 @@ SUBDIRS= .
+ .SUFFIXES:.c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
+
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+ bcftools:lib $(AOBJS)
+- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
+
+ bcf.o:bcf.h
+ vcf.o:bcf.h
+diff --git a/misc/Makefile b/misc/Makefile
+index d36e7ac..7ae1dc3 100644
+--- a/misc/Makefile
++++ b/misc/Makefile
+@@ -1,8 +1,8 @@
+-CC= gcc
+-CXX= g++
+-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
+-CXXFLAGS= $(CFLAGS)
+-DFLAGS= -D_FILE_OFFSET_BITS=64
++CC?= gcc
++CXX?= g++
++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
++CXXFLAGS?= $(CFLAGS)
++CPPFLAGS+= -D_FILE_OFFSET_BITS=64
+ OBJS=
+ PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
+ INCLUDES= -I..
+@@ -11,7 +11,7 @@ SUBDIRS= .
+ .SUFFIXES:.c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ all:$(PROG)
+
+@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+ lib:
+
+ bamcheck:bamcheck.o
+- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
+
+ bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+ $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
+
+ ace2sam:ace2sam.o
+- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz
+
+ wgsim:wgsim.o
+- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz
+
+ md5fa:md5.o md5fa.o md5.h ../kseq.h
+- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz
+
+ md5sum-lite:md5sum-lite.o
+- $(CC) $(CFLAGS) -o $@ md5sum-lite.o
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o
+
+ md5sum-lite.o:md5.c md5.h
+ $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+
+ maq2sam-short:maq2sam.c
+- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz
+
+ maq2sam-long:maq2sam.c
+- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
++ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz
+
+ md5fa.o:md5.h md5fa.c
+ $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch
new file mode 100644
index 000000000000..53a8b66f918f
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch
@@ -0,0 +1,59 @@
+ Makefile | 26 ++++++++++++++++++--------
+ 1 file changed, 18 insertions(+), 8 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index ae59abf..0d2788c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-CPPFLAGS = $(DFLAGS) $(INCLUDES)
+-CFLAGS = -g -Wall -O2
+-LDFLAGS =
+-LDLIBS =
++CC ?= gcc
++CPPFLAGS += $(DFLAGS) $(INCLUDES)
++CFLAGS ?= -g -Wall -O2
++LDFLAGS +=
++LDLIBS +=
++BAMLIB ?= libbam.a
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \
+ sam_header.o bam_plbuf.o
+@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
+ prefix = /usr/local
+ exec_prefix = $(prefix)
+ bindir = $(exec_prefix)/bin
++bindir = $(exec_prefix)/lib
+ mandir = $(prefix)/share/man
+ man1dir = $(mandir)/man1
+
+@@ -115,14 +117,22 @@ version.h:
+ .c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+
++$(LOBJS):
++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+
+-lib:libbam.a
++
++lib:libbam.a libbam.so.1.0
+
+ libbam.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
++libbam.so.1.0:$(LOBJS)
++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++ ln -sf $@ libbam.so.0
++ ln -sf $@ libbam.so
++
++samtools: $(AOBJS) $(HTSLIB) lib
++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
new file mode 100644
index 000000000000..b9ae77de67d2
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
@@ -0,0 +1,153 @@
+ Makefile | 76 ++++++++++++++++++++++++++++++++++++----------------------------
+ 1 file changed, 43 insertions(+), 33 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 43cefc3..743dd07 100644
+--- a/Makefile
++++ b/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-CPPFLAGS = $(DFLAGS) $(INCLUDES)
+-CFLAGS = -g -Wall -O2
+-LDFLAGS =
+-LDLIBS =
++CC ?= gcc
++CPPFLAGS += $(DFLAGS) $(INCLUDES)
++CFLAGS ?= -g -Wall -O2
++LDFLAGS +=
++LDLIBS +=
++BAMLIB ?= libbam.a
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \
+ sam_header.o bam_plbuf.o
+@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
+ prefix = /usr/local
+ exec_prefix = $(prefix)
+ bindir = $(exec_prefix)/bin
++libdir = $(exec_prefix)/lib
+ mandir = $(prefix)/share/man
+ man1dir = $(mandir)/man1
+
+@@ -115,63 +117,71 @@ version.h:
+ .c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+
++$(LOBJS):
++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+
+-lib:libbam.a
++
++lib:libbam.a libbam.so.1.0
+
+ libbam.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
++libbam.so.1.0:$(LOBJS)
++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++ ln -sf $@ libbam.so.0
++ ln -sf $@ libbam.so
++
++samtools: $(AOBJS) lib
++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h)
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h)
+ sam_h = sam.h $(htslib_sam_h) $(bam_h)
+-sample_h = sample.h $(HTSDIR)/htslib/kstring.h
++sample_h = sample.h
+
+ bam.o: bam.c $(bam_h) sam_header.h
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h
++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
+ bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h
+ bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
+ bam_aux.o: bam_aux.c
+ bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
+ bam_color.o: bam_color.c $(bam_h)
+-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
+-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
+-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h
++bam_import.o: bam_import.c $(bam_h)
++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h)
++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h)
+ bam_mate.o: bam_mate.c $(bam_h)
+ bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h
+ bam_pileup.o: bam_pileup.c $(sam_h)
+ bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
+-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
+ bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
+-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
+-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
+-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h)
++bam_rmdup.o: bam_rmdup.c $(sam_h)
++bam_rmdupse.o: bam_rmdupse.c $(sam_h)
++bam_sort.o: bam_sort.c $(htslib_sam_h)
+ bam_stat.o: bam_stat.c $(bam_h) samtools.h
+ bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
+ bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
+ bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
+ bam_flags.o: bam_flags.c $(sam_h)
+-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
+ bamtk.o: bamtk.c $(bam_h) version.h samtools.h
+-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
+-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
++bedcov.o: bedcov.c $(htslib_sam_h)
++bedidx.o: bedidx.c
+ cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
+-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
++errmod.o: errmod.c errmod.h
+ kaln.o: kaln.c kaln.h
+ kprobaln.o: kprobaln.c kprobaln.h
+ padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
+-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
++phase.o: phase.c $(htslib_sam_h) errmod.h
+ sam.o: sam.c $(htslib_faidx_h) $(sam_h)
+-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h
+-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
+-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
+-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
+-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)
++sam_header.o: sam_header.c sam_header.h
++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h
++sample.o: sample.c $(sample_h)
++stats_isize.o: stats_isize.c stats_isize.h
++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h)
+
+
+ # test programs
+@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib
+ # For tests that might use it, set $REF_PATH explicitly to use only reference
+ # areas within the test suite (or set it to ':' to use no reference areas).
+ # (regression.sh sets $REF_PATH to a subdirectory itself.)
+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
+- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
++check test: samtools $(BUILT_TEST_PROGRAMS)
++ REF_PATH=: test/test.pl --exec bgzip=bgzip
+ test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+ test/merge/test_pretty_header
+ test/merge/test_rtrans_build
+@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
+ misc/wgsim: misc/wgsim.o
+ $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
+
+-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
++misc/ace2sam.o: misc/ace2sam.c
+ misc/md5.o: misc/md5.c misc/md5.h
+-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
+-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
++misc/md5fa.o: misc/md5fa.c misc/md5.h
++misc/wgsim.o: misc/wgsim.c
+
+ misc/maq2sam-short.o: misc/maq2sam.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch
new file mode 100644
index 000000000000..2343b2245a29
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch
@@ -0,0 +1,193 @@
+ Makefile | 94 +++++++++++++++++++++++++++++++++++-----------------------------
+ 1 file changed, 52 insertions(+), 42 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e368cee..9054526 100644
+--- a/Makefile
++++ b/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-CPPFLAGS = $(DFLAGS) $(INCLUDES)
+-CFLAGS = -g -Wall -O2
+-LDFLAGS =
+-LDLIBS =
++CC ?= gcc
++CPPFLAGS += $(DFLAGS) $(INCLUDES)
++CFLAGS ?= -g -Wall -O2
++LDFLAGS +=
++LDLIBS +=
++BAMLIB ?= libbam.a
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \
+ sam_header.o bam_plbuf.o
+@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
+ prefix = /usr/local
+ exec_prefix = $(prefix)
+ bindir = $(exec_prefix)/bin
++libdir = $(exec_prefix)/lib
+ mandir = $(prefix)/share/man
+ man1dir = $(mandir)/man1
+
+@@ -115,62 +117,70 @@ version.h:
+ .c.o:
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+
++$(LOBJS):
++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+
+-lib:libbam.a
++
++lib:libbam.a libbam.so.1.0
+
+ libbam.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
++libbam.so.1.0:$(LOBJS)
++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++ ln -sf $@ libbam.so.0
++ ln -sf $@ libbam.so
++
++samtools: $(AOBJS) lib
++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h)
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h)
+ sam_h = sam.h $(htslib_sam_h) $(bam_h)
+-sample_h = sample.h $(HTSDIR)/htslib/kstring.h
++sample_h = sample.h
+
+ bam.o: bam.c $(bam_h) sam_header.h
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h
++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
+ bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
+ bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
+ bam_aux.o: bam_aux.c
+ bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
+ bam_color.o: bam_color.c $(bam_h)
+-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
+-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
+-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h
++bam_import.o: bam_import.c $(bam_h)
++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h)
++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h)
+ bam_mate.o: bam_mate.c $(bam_h)
+ bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h
+ bam_pileup.o: bam_pileup.c $(sam_h)
+ bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
+-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
+ bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
+-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
+-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
+-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h)
++bam_rmdup.o: bam_rmdup.c $(sam_h)
++bam_rmdupse.o: bam_rmdupse.c $(sam_h)
++bam_sort.o: bam_sort.c $(htslib_sam_h)
+ bam_stat.o: bam_stat.c $(bam_h) samtools.h
+ bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
+ bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
+ bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
+ bam_flags.o: bam_flags.c $(sam_h)
+-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
+ bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h
+-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
+-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
++bedcov.o: bedcov.c $(htslib_sam_h)
++bedidx.o: bedidx.c
+ cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
+-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
++errmod.o: errmod.c errmod.h
+ kprobaln.o: kprobaln.c kprobaln.h
+ padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
+-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
++phase.o: phase.c $(htslib_sam_h) errmod.h
+ sam.o: sam.c $(htslib_faidx_h) $(sam_h)
+-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h
+-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
+-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
+-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
+-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)
++sam_header.o: sam_header.c sam_header.h
++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h
++sample.o: sample.c $(sample_h)
++stats_isize.o: stats_isize.c stats_isize.h
++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h)
+
+
+ # test programs
+@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib
+ # For tests that might use it, set $REF_PATH explicitly to use only reference
+ # areas within the test suite (or set it to ':' to use no reference areas).
+ # (regression.sh sets $REF_PATH to a subdirectory itself.)
+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
+- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
++check test: samtools $(BUILT_TEST_PROGRAMS)
++ REF_PATH=: test/test.pl --exec bgzip=bgzip
+ test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+ test/merge/test_pretty_header
+ test/merge/test_rtrans_build
+@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
+ test/split/test_parse_args
+
+
+-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB)
++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB)
++test/merge/test_pretty_header: test/merge/test_pretty_header.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB)
++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB)
++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB)
++test/split/test_count_rg: test/split/test_count_rg.o test/test.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB)
++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB)
++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB)
++test/split/test_parse_args: test/split/test_parse_args.o test/test.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz
+
+-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
++test/vcf-miniview: test/vcf-miniview.o
+ $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz
+
+ test_test_h = test/test.h $(htslib_sam_h)
+@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
+ misc/wgsim: misc/wgsim.o
+ $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
+
+-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
++misc/ace2sam.o: misc/ace2sam.c
+ misc/md5.o: misc/md5.c misc/md5.h
+-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
+-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
++misc/md5fa.o: misc/md5fa.c misc/md5.h
++misc/wgsim.o: misc/wgsim.c
+
+ misc/maq2sam-short.o: misc/maq2sam.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml
new file mode 100644
index 000000000000..74dc02bc9826
--- /dev/null
+++ b/sci-biology/samtools/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">samtools</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild
new file mode 100644
index 000000000000..34720e4b9abb
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.12.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+MY_P="${P}a"
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://samtools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i 's/^CFLAGS=/CFLAGS+=/' "${S}"/{Makefile,misc/Makefile}
+}
+
+src_install() {
+ dobin samtools || die
+ dobin $(find misc -type f -executable) || die
+ insinto /usr/share/${PN}
+ doins -r examples || die
+ doman ${PN}.1 || die
+ dodoc AUTHORS ChangeLog NEWS
+}
diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
new file mode 100644
index 000000000000..133ababad9cc
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://samtools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="sys-libs/ncurses"
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ tc-export CC AR
+}
+
+src_compile() {
+ local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ emake dylib LIBCURSES="${_ncurses}"
+ emake LIBCURSES="${_ncurses}"
+}
+
+src_install() {
+ dobin samtools $(find bcftools misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+
+ dolib.so libbam$(get_libname 1)
+ dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname)
+
+ insinto /usr/include/bam
+ doins *.h
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild
new file mode 100644
index 000000000000..802aefc91ada
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.0-r1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses
+ sci-libs/htslib"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-1.0 -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ dolib.so libbam.so*
+
+ insinto /usr/include/bam
+ doins *.h
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild
new file mode 100644
index 000000000000..d1f1f507b45c
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.0.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses
+ sci-libs/htslib"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-1.0 -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ CC="$(tc-getCC)"
+ LDFLAGS="${LDFLAGS}"
+ CFLAGS="${CFLAGS}"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild
new file mode 100644
index 000000000000..1f5b82ab4602
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses
+ ~sci-libs/htslib-${PV}"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-* -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_test() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ dolib.so libbam.so*
+
+ insinto /usr/include/bam
+ doins *.h
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild
new file mode 100644
index 000000000000..3a999e01e865
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.2.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses
+ >=sci-libs/htslib-${PV}"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-* -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_test() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ dolib.so libbam.so*
+
+ insinto /usr/include/bam
+ doins *.h
+
+ doman ${PN}.1
+ dodoc AUTHORS NEWS README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r examples
+ fi
+}
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
new file mode 100644
index 000000000000..6bb12c484533
--- /dev/null
+++ b/sci-biology/seaview/Manifest
@@ -0,0 +1 @@
+DIST seaview_4.3.5.tar.gz 309530 SHA256 38050d6792eb799d61e5e849f76971a9c7d45f467e5c04fbc4363062d8e7100d SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a WHIRLPOOL 82fc7324bf1d934d69712629808d6b4178a5f2cdcf25351fb2fe2784f9cea0c1ec0aaaba7a3a08c84795108eb049394ceaab052af8cc0efbb0975064fa4e80e0
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
new file mode 100644
index 000000000000..33794f43ab01
--- /dev/null
+++ b/sci-biology/seaview/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ SeaView is a graphical multiple sequence alignment editor developped by
+ Manolo Gouy. SeaView is able to read and write various alignment
+ formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
+ manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
+ programs to locally improve the alignment.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/seaview/seaview-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild
new file mode 100644
index 000000000000..00abeb426064
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.3.5.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A graphical multiple sequence alignment editor"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE="+xft"
+
+CDEPEND="
+ sys-libs/zlib
+ x11-libs/fltk:1
+ x11-libs/libX11
+ xft? (
+ x11-libs/libXft
+ x11-libs/fltk:1[xft] )"
+RDEPEND="${CDEPEND}
+ sci-biology/clustalw
+ || ( sci-libs/libmuscle sci-biology/muscle )
+ sci-biology/phyml"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+ # respect CXXFLAGS (package uses them as CFLAGS)
+ sed \
+ -e "s:^CC.*:CC = $(tc-getCC):" \
+ -e "s:^CXX.*:CXX = $(tc-getCXX):" \
+ -e "s:\$(OPT):${CXXFLAGS}:" \
+ -e "s:^OPT:#OPT:" \
+ -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
+ -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
+ -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+ -e "s:^USE_XFT:#USE_XFT:" \
+ -e "s:^#HELPFILE:HELPFILE:" \
+ -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
+ -e "s:^#PHYMLNAME:PHYMLNAME:" \
+ -e 's:-lXinerama::g' \
+ -e 's:-lpng::g' \
+ -e 's:-ljpeg::g' \
+ -e 's:-lfontconfig::g' \
+ -i Makefile || die "sed failed while editing Makefile"
+
+ if use xft; then
+ sed \
+ -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
+ -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
+ -i Makefile || die "sed failed while editing Makefile to enable xft"
+ else
+ sed -i -e "s:-lXft::" Makefile || die
+ fi
+}
+
+src_install() {
+ dobin seaview
+
+ # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
+ insinto /usr/share/seaview
+ doins example.nxs seaview.html
+
+ insinto /usr/share/seaview/images
+ doins seaview.xpm
+
+ make_desktop_entry seaview Seaview
+
+ doman seaview.1
+}
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
new file mode 100644
index 000000000000..134871573387
--- /dev/null
+++ b/sci-biology/seqan/Manifest
@@ -0,0 +1,3 @@
+DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b
+DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
+DIST seqan-src-2.0.0.tar.gz 115731415 SHA256 69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512 9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a WHIRLPOOL afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 000000000000..0f438ff07bce
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+ set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+
+ # enable static linkage for seqan apps
+- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+- endif ()
++# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++# endif ()
+
+ # Get all direct entries of the current source directory into ENTRIES.
+ file (GLOB ENTRIES
diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
new file mode 100644
index 000000000000..de14e9d58b8e
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
@@ -0,0 +1,15 @@
+ include/seqan/stream/zipstream/zutil.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/seqan/stream/zipstream/zutil.h b/include/seqan/stream/zipstream/zutil.h
+index 2806344..f8b41e6 100644
+--- a/include/seqan/stream/zipstream/zutil.h
++++ b/include/seqan/stream/zipstream/zutil.h
+@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */
+
+ /* functions */
+
++#define OF(x) x
+ #ifdef HAVE_STRERROR
+ extern char *strerror OF((int));
+ # define zstrerror(errnum) strerror(errnum)
diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/seqan/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/seqan/seqan-1.3.1-r1.ebuild b/sci-biology/seqan/seqan-1.3.1-r1.ebuild
new file mode 100644
index 000000000000..a74eac3ccfce
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.3.1-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://ftp.seqan.de/releases/${P}.zip"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+ sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${P}/cmake
+
+src_prepare() {
+ append-cppflags -I"${EPREFIX}/usr/include/bam"
+ rm -rf "${S}"/../lib/samtools || die
+
+ sed \
+ -e "s:docs:docs/.:g" \
+ -e "/DESTINATION/s:seqan:doc/${PF}/html:g" \
+ -i CMakeLists.txt || die
+
+ sed \
+ -e "/DESTINATION/s:bin):share/${PN}):g" \
+ -i apps/CMakeLists.txt || die
+
+ cmake-utils_src_prepare
+}
diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild
new file mode 100644
index 000000000000..a7e436a2013b
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+ sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-shared.patch
+ "${FILESDIR}"/${P}-include.patch
+)
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} = "binary" ]] && return 0
+ if use amd64; then
+ if ! echo "#include <smmintrin.h>" | gcc -E - 2>&1 > /dev/null; then
+ ewarn "Need at least SSE4.1 support"
+ die "Missing SSE4.1 support"
+ fi
+ fi
+}
+
+src_prepare() {
+ rm -f \
+ util/cmake/FindZLIB.cmake \
+ || die
+ touch extras/apps/seqan_flexbar/README || die
+ sed \
+ -e "s:share/doc:share/doc/${PF}:g" \
+ -i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DBoost_NO_BOOST_CMAKE=ON
+ )
+ cmake-utils_src_configure
+}
+
+src_install() {
+ mkdir -p "${BUILD_DIR}"/docs/html || die
+ cmake-utils_src_install
+ chmod 755 "${ED}"/usr/bin/*sh || die
+
+ mv "${ED}"/usr/bin/{,seqan-}join || die
+}
+
+pkg_postinst() {
+ elog "Due to filecollision the 'join' binary has been renamed to seqan-join"
+}
diff --git a/sci-biology/seqan/seqan-2.0.0.ebuild b/sci-biology/seqan/seqan-2.0.0.ebuild
new file mode 100644
index 000000000000..5437e6df9f5b
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.0.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse4_1"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1"
+
+RDEPEND="${PYTHON_DEPS}
+ dev-libs/boost:=
+ sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${PN}-${PN}-v${PV}
+
+PATCHES=(
+ "${FILESDIR}"/${P}-zlib.patch
+)
+
+src_prepare() {
+ rm -f \
+ util/cmake/FindZLIB.cmake \
+ || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DBoost_NO_BOOST_CMAKE=ON
+ )
+ cmake-utils_src_configure
+}
+
+src_install() {
+ mkdir -p "${BUILD_DIR}"/docs/html || die
+ cmake-utils_src_install
+ chmod 755 "${ED}"/usr/bin/*sh || die
+}
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
new file mode 100644
index 000000000000..ad017d9fc592
--- /dev/null
+++ b/sci-biology/shrimp/Manifest
@@ -0,0 +1,2 @@
+DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
+DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/shrimp/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
new file mode 100644
index 000000000000..771432f0bada
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="shrimp"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="custom-cflags"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="
+ !sci-biology/emboss
+ !sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+ if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then
+ elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+ die "C compiler lacks OPENMP support"
+ fi
+}
+
+src_prepare() {
+ sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+ # respect LDFLAGS wrt 331823
+ sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+ -e 's/-static//' Makefile || die
+}
+
+src_compile() {
+ append-flags -fopenmp
+ use custom-cflags || append-flags -O3 # per instructions in BUILDING
+ tc-export CXX
+ emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ rm bin/README
+ dobin bin/*
+ insinto /usr/share/${PN}
+ doins -r utils
+ dodoc HISTORY README TODO SPLITTING_AND_MERGING
+}
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
new file mode 100644
index 000000000000..7f2033d9054a
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit flag-o-matic python-single-r1 toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="shrimp"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags +cpu_flags_x86_sse2"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}
+ ${PYTHON_DEPS}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_pretend() {
+ use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
+}
+
+pkg_setup() {
+ if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then
+ elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+ die "C compiler lacks OPENMP support"
+ fi
+ python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ sed \
+ -e '1 a #include <stdint.h>' \
+ -i common/dag_glue.cpp || die
+ # respect LDFLAGS wrt 331823
+ sed \
+ -e "s/LDFLAGS/LIBS/" \
+ -e "s/\$(LD)/& \$(LDFLAGS)/" \
+ -e 's/-static//' \
+ -i Makefile || die
+
+ append-flags -fopenmp
+ if ! use custom-cflags; then
+ append-flags -O3
+ replace-flags -O* -O3
+ fi
+ tc-export CXX
+
+ cd utils || die
+ sed -e '/^#!/d' -i *py || die
+ sed -e '1i#!/usr/bin/python' -i *py || die
+}
+
+src_compile() {
+ emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+ local i
+ newdoc bin/README README.bin && rm bin/README
+ dobin bin/* utils/split-contigs utils/temp-sink
+ dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
+
+ pushd utils > /dev/null
+
+ python_doscript *py
+
+ rm *.py *.o *.c split-contigs temp-sink || die
+ insinto /usr/share/${PN}
+ doins -r *
+}
diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest
new file mode 100644
index 000000000000..3a0be49f2116
--- /dev/null
+++ b/sci-biology/sibsim4/Manifest
@@ -0,0 +1 @@
+DIST SIBsim4-0.20.tar.gz 32118 SHA256 ee02ae5f678d6843cf3ba267140dfccf9648a60d1f01263ae70d405723a35463 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8 WHIRLPOOL b6117192170a7c8b6bcc441c8b31b392410116d25045203ce33e5274a0a65608de408626df5a29fddbbbe34973869b055603defd58d06cbc6240925556b63282
diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml
new file mode 100644
index 000000000000..cfcd5be131d0
--- /dev/null
+++ b/sci-biology/sibsim4/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">sibsim4</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild
new file mode 100644
index 000000000000..ecef6870dea4
--- /dev/null
+++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner"
+HOMEPAGE="http://sibsim4.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/SIBsim4-${PV}"
+
+src_prepare() {
+ sed \
+ -e 's/CFLAGS = /CFLAGS +=/' \
+ -e '/^CC/s:=:?=:' \
+ -e '/^OPT/d' \
+ -e "s:-o:${LDFLAGS} -o:g" \
+ -i "${S}/Makefile" || die
+ tc-export CC
+}
+
+src_install() {
+ dobin SIBsim4
+ doman SIBsim4.1
+}
diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
new file mode 100644
index 000000000000..f2a25200b895
--- /dev/null
+++ b/sci-biology/sim4/Manifest
@@ -0,0 +1 @@
+DIST sim4.tar.gz 60814 RMD160 5acad71daa94893025a21b73b416dd3903078be5 SHA1 11a9170ea03990268d409056084415d725c6290b SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
new file mode 100644
index 000000000000..ea9731279003
--- /dev/null
+++ b/sci-biology/sim4/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ sim4 is a similarity-based tool for aligning an expressed DNA sequence
+ (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
+ end matches when the two input sequences overlap at one end (i.e., the
+ start of one sequence overlaps the end of the other).sim4 employs a
+ blast-based technique to first determine the basic matching blocks
+ representing the "exon cores". In this first stage, it detects all
+ possible exact matches of W-mers (i.e., DNA words of size W) between
+ the two sequences and extends them to maximal scoring gap-free
+ segments. In the second stage, the exon cores are extended into the
+ adjacent as-yet-unmatched fragments using greedy alignment algorithms,
+ and heuristics are used to favor configurations that conform to the
+ splice-site recognition signals (GT-AG, CT-AC). If necessary, the
+ process is repeated with less stringent parameters on the unmatched
+ fragments.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/sim4/sim4-20030921-r1.ebuild b/sci-biology/sim4/sim4-20030921-r1.ebuild
new file mode 100644
index 000000000000..178bf92ab5da
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921-r1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit toolchain-funcs
+
+DESCRIPTION="A program to align cDNA and genomic DNA"
+HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
+SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+S=${WORKDIR}/${PN}.2003-09-21
+
+src_compile() {
+ echo "$(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm"
+ $(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm || die
+}
+
+src_install() {
+ dobin ${PN} || die
+ dodoc README.* VERSION || die
+}
diff --git a/sci-biology/sim4/sim4-20030921.ebuild b/sci-biology/sim4/sim4-20030921.ebuild
new file mode 100644
index 000000000000..12d5231aa120
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A program to align cDNA and genomic DNA"
+HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
+SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE=""
+
+S="${WORKDIR}/${PN}.2003-09-21"
+
+src_install() {
+ dobin sim4 || die
+ dodoc README.psublast README.sim4 VERSION || die
+}
diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest
new file mode 100644
index 000000000000..370468a92b39
--- /dev/null
+++ b/sci-biology/snpfile/Manifest
@@ -0,0 +1 @@
+DIST snpfile-2.0.1.tar.gz 171854 SHA256 71569e0dcd426447d1a5d215fb47615074a4c8d935cf70ef63c5f47a411b0b76
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
new file mode 100644
index 000000000000..2b79c2492ede
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
@@ -0,0 +1,12 @@
+diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh
+--- snpfile-2.0.1.orig/input_archive.hh 2008-05-03 17:25:44.000000000 +0300
++++ snpfile-2.0.1/input_archive.hh 2009-07-26 21:26:10.000000000 +0300
+@@ -26,6 +26,8 @@
+ #ifndef INPUT_ARCHIVE_HH_INCLUDED
+ #define INPUT_ARCHIVE_HH_INCLUDED
+
++#include <stdint.h>
++
+ #include <string>
+
+ #include "archive_common.hh"
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
new file mode 100644
index 000000000000..e6a8d60ec69c
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
@@ -0,0 +1,533 @@
+Fixing as-needed issues, provide shared libs
+
+https://bugs.gentoo.org/show_bug.cgi?id=294971
+
+--- Makefile.am
++++ Makefile.am
+@@ -1,440 +1,92 @@
+ ACLOCAL_AMFLAGS = -I m4
+
+-AM_CXXFLAGS =
+-AM_CXXFLAGS += -Wall
+-AM_CXXFLAGS += $(BOOST_CPPFLAGS)
++AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS)
++SUFFIXES = .cc
+
+-
+-# for testing
+-AM_CXXFLAGS += -g -O2 #-lefence
+-
+-# for profiling
+-#CXXFLAGS += -O3 -g -pg
+-#AM_CXXFLAGS += -O3 -g -pg
+-
+-# for production
+-#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
+-#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
+-
+-# for coverage testing
+-#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
+-#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
+-
+-
+-lib_LIBRARIES = libsnpfile.a
++lib_LTLIBRARIES = libsnpfile.la
+
+ noinst_PROGRAMS =
+-TESTS =
+-EXTRA_DIST =
+-bin_PROGRAMS =
+
+ # conversion tools
+-bin_PROGRAMS += text2snpfile
+-bin_PROGRAMS += snpfile2text
+-bin_PROGRAMS += snpfile2fastPHASE
+-bin_PROGRAMS += fastPHASE2snpfile
+-bin_PROGRAMS += snpfile2haploview
+-bin_PROGRAMS += beagle_phase_snpfile
++bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \
++ snpfile2haploview beagle_phase_snpfile
+
+ # data extraction tools
+-bin_PROGRAMS += snpfile_genotype_count
+-bin_PROGRAMS += snpfile_phenotypes
+-bin_PROGRAMS += snpfile_markers
+-
+-bin_PROGRAMS += snpfile_metadata_info
+-bin_PROGRAMS += snpfile_set_metadata
+-bin_PROGRAMS += snpfile_get_metadata
++bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers
++
++bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata
+
+ # other tools
+ noinst_PROGRAMS += snpfile_split_on_column
+
+ # tests
+-noinst_PROGRAMS += matrix_test
+-TESTS += matrix_test
+-noinst_PROGRAMS += file_test
+-TESTS += file_test
+-noinst_PROGRAMS += file_matrix_test
+-TESTS += file_matrix_test
+-noinst_PROGRAMS += readonly_matrix_test
+-TESTS += readonly_matrix_test
+-noinst_PROGRAMS += archives_test
+-TESTS += archives_test
+-noinst_PROGRAMS += metadata_access_test
+-TESTS += metadata_access_test
+-noinst_PROGRAMS += metadata_types_test
+-TESTS += metadata_types_test
+-noinst_PROGRAMS += iterators_test
+-TESTS += iterators_test
+-noinst_PROGRAMS += tabulate_test
+-TESTS += tabulate_test
+-noinst_PROGRAMS += metadata_filtering_test
+-TESTS += metadata_filtering_test
++TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \
++ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test
++
++noinst_PROGRAMS += $(TESTS)
+
+ #Utils for testing across different machines
+-noinst_PROGRAMS += make_test_snpfile
+-noinst_PROGRAMS += test_test_snpfile
++noinst_PROGRAMS += make_test_snpfile test_test_snpfile
+
+ # other experiments...
+-noinst_PROGRAMS += row_metadata_experiment
+-noinst_PROGRAMS += metadata_cache_prototype
+-noinst_PROGRAMS += matrix_benchmark
+-noinst_PROGRAMS += matrix_benchmark_write
+-noinst_PROGRAMS += matrix_benchmark_read
+-
+-
+-
+-matrix_test_LDADD =
+-matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
+-matrix_test_SOURCES =
+-matrix_test_SOURCES += test_util.hh test_util.cc
+-matrix_test_SOURCES += matrix.hh matrix.cc
+-matrix_test_SOURCES += array_matrix.hh array_matrix.cc
+-matrix_test_SOURCES += file_matrix.hh file_matrix.cc
+-matrix_test_SOURCES += input_archive.hh
+-matrix_test_SOURCES += output_archive.hh
+-matrix_test_SOURCES += metadata.hh metadata.cc
+-matrix_test_SOURCES += snpfile.hh snpfile.cc
+-matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-matrix_test_SOURCES += matrix_test.cc
+-
+-
+-file_test_LDADD =
+-file_test_LDADD += $(BOOST_SIGNALS_LIB)
+-file_test_SOURCES =
+-file_test_SOURCES += test_util.hh test_util.cc
+-file_test_SOURCES += metadata.hh metadata.cc
+-file_test_SOURCES += snpfile.hh snpfile.cc
+-file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-file_test_SOURCES += file_test.cc
+-file_test_SOURCES += metadata_access.hh
+-file_test_SOURCES += input_archive.hh
+-file_test_SOURCES += output_archive.hh
+-
+-file_matrix_test_LDADD =
+-file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
+-file_matrix_test_SOURCES =
+-file_matrix_test_SOURCES += test_util.hh test_util.cc
+-file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
+-file_matrix_test_SOURCES += matrix.hh matrix.cc
+-file_matrix_test_SOURCES += input_archive.hh
+-file_matrix_test_SOURCES += output_archive.hh
+-file_matrix_test_SOURCES += metadata.hh metadata.cc
+-file_matrix_test_SOURCES += snpfile.hh snpfile.cc
+-file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-file_matrix_test_SOURCES += file_matrix_test.cc
+-
+-
+-readonly_matrix_test_LDADD =
+-readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
+-readonly_matrix_test_SOURCES =
+-readonly_matrix_test_SOURCES += test_util.hh test_util.cc
+-readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc
+-readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
+-readonly_matrix_test_SOURCES += matrix.hh matrix.cc
+-readonly_matrix_test_SOURCES += input_archive.hh
+-readonly_matrix_test_SOURCES += output_archive.hh
+-readonly_matrix_test_SOURCES += metadata.hh metadata.cc
+-readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc
+-readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-readonly_matrix_test_SOURCES += readonly_matrix_test.cc
+-
+-
+-archives_test_SOURCES =
+-archives_test_SOURCES += input_archive.hh
+-archives_test_SOURCES += output_archive.hh
+-archives_test_SOURCES += archives_test.cc
+-
+-
+-metadata_access_test_LDADD =
+-metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB)
+-metadata_access_test_SOURCES =
+-metadata_access_test_SOURCES += test_util.hh test_util.cc
+-metadata_access_test_SOURCES += metadata.hh metadata.cc
+-metadata_access_test_SOURCES += snpfile.hh snpfile.cc
+-metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-metadata_access_test_SOURCES += input_archive.hh
+-metadata_access_test_SOURCES += output_archive.hh
+-metadata_access_test_SOURCES += serialization_trait.hh
+-metadata_access_test_SOURCES += metadata_access_test.cc
+-
+-
+-metadata_types_test_LDADD =
+-metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB)
+-metadata_types_test_SOURCES =
+-metadata_types_test_SOURCES += test_util.hh test_util.cc
+-metadata_types_test_SOURCES += metadata.hh metadata.cc
+-metadata_types_test_SOURCES += snpfile.hh snpfile.cc
+-metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-metadata_types_test_SOURCES += input_archive.hh
+-metadata_types_test_SOURCES += output_archive.hh
+-metadata_types_test_SOURCES += serialization_trait.hh
+-metadata_types_test_SOURCES += metadata_types_test.cc
+-
+-
+-iterators_test_SOURCES =
+-iterators_test_SOURCES += iterators.hh
+-iterators_test_SOURCES += array_matrix.hh array_matrix.cc
+-iterators_test_SOURCES += matrix.hh matrix.cc
+-iterators_test_SOURCES += iterators_test.cc
+-
+-
+-tabulate_test_SOURCES =
+-tabulate_test_SOURCES += tabulate.hh
+-tabulate_test_SOURCES += array_matrix.hh array_matrix.cc
+-tabulate_test_SOURCES += matrix.hh matrix.cc
+-tabulate_test_SOURCES += tabulate_test.cc
+-
+-
+-metadata_filtering_test_SOURCES =
+-metadata_filtering_test_SOURCES += matrix.hh matrix.cc
+-metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc
+-metadata_filtering_test_SOURCES += metadata_filtering.hh
+-metadata_filtering_test_SOURCES += metadata_filtering_test.cc
+-
+-
+-make_test_snpfile_LDADD =
+-make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
+-make_test_snpfile_SOURCES =
+-make_test_snpfile_SOURCES += metadata.hh metadata.cc
+-make_test_snpfile_SOURCES += snpfile.hh snpfile.cc
+-make_test_snpfile_SOURCES += matrix.hh matrix.cc
+-make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
+-make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-make_test_snpfile_SOURCES += input_archive.hh
+-make_test_snpfile_SOURCES += output_archive.hh
+-make_test_snpfile_SOURCES += make_test_snpfile.cc
+-
+-
+-test_test_snpfile_LDADD =
+-test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
+-test_test_snpfile_SOURCES =
+-test_test_snpfile_SOURCES += metadata.hh metadata.cc
+-test_test_snpfile_SOURCES += snpfile.hh snpfile.cc
+-test_test_snpfile_SOURCES += matrix.hh matrix.cc
+-test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
+-test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-test_test_snpfile_SOURCES += input_archive.hh
+-test_test_snpfile_SOURCES += output_archive.hh
+-test_test_snpfile_SOURCES += test_test_snpfile.cc
+-
+-
+-row_metadata_experiment_LDADD =
+-row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB)
+-row_metadata_experiment_SOURCES =
+-row_metadata_experiment_SOURCES += matrix.hh matrix.cc
+-row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc
+-row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc
+-row_metadata_experiment_SOURCES += input_archive.hh
+-row_metadata_experiment_SOURCES += output_archive.hh
+-row_metadata_experiment_SOURCES += metadata.hh metadata.cc
+-row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc
+-row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-row_metadata_experiment_SOURCES += test_util.hh test_util.cc
+-row_metadata_experiment_SOURCES += row_metadata_experiment.cc
+-
+-
+-metadata_cache_prototype_SOURCES =
+-metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc
+-metadata_cache_prototype_LDFLAGS =
+-metadata_cache_prototype_LDFLAGS += -L.
+-metadata_cache_prototype_LDADD =
+-metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB)
+-metadata_cache_prototype_LDADD += -lsnpfile
+-
+-
+-matrix_benchmark_LDADD =
+-matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB)
+-matrix_benchmark_SOURCES =
+-matrix_benchmark_SOURCES += test_util.hh test_util.cc
+-matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc
+-matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc
+-matrix_benchmark_SOURCES += matrix.hh matrix.cc
+-matrix_benchmark_SOURCES += input_archive.hh
+-matrix_benchmark_SOURCES += output_archive.hh
+-matrix_benchmark_SOURCES += metadata.hh metadata.cc
+-matrix_benchmark_SOURCES += snpfile.hh snpfile.cc
+-matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-matrix_benchmark_SOURCES += timing.hh timing.cc
+-matrix_benchmark_SOURCES += matrix_benchmark.cc
+-
+-
+-matrix_benchmark_write_LDADD =
+-matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB)
+-matrix_benchmark_write_SOURCES =
+-matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc
+-matrix_benchmark_write_SOURCES += matrix.hh matrix.cc
+-matrix_benchmark_write_SOURCES += input_archive.hh
+-matrix_benchmark_write_SOURCES += output_archive.hh
+-matrix_benchmark_write_SOURCES += metadata.hh metadata.cc
+-matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc
+-matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-matrix_benchmark_write_SOURCES += timing.hh timing.cc
+-matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc
+-
+-
+-matrix_benchmark_read_LDADD =
+-matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB)
+-matrix_benchmark_read_SOURCES =
+-matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc
+-matrix_benchmark_read_SOURCES += matrix.hh matrix.cc
+-matrix_benchmark_read_SOURCES += input_archive.hh
+-matrix_benchmark_read_SOURCES += output_archive.hh
+-matrix_benchmark_read_SOURCES += metadata.hh metadata.cc
+-matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc
+-matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc
+-matrix_benchmark_read_SOURCES += timing.hh timing.cc
+-matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc
++noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
++ matrix_benchmark_write matrix_benchmark_read
++
++LDADD = $(top_builddir)/libsnpfile.la
++
++matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
++
++file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \
++ output_archive.hh
++
++file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
++ file_matrix_test.cc
++
++readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
++ readonly_matrix_test.cc
+
++archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc
++
++metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
++ serialization_trait.hh metadata_access_test.cc
++
++metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
++ serialization_trait.hh metadata_types_test.cc
++
++iterators_test_SOURCES = iterators.hh iterators_test.cc
++
++tabulate_test_SOURCES = tabulate.hh tabulate_test.cc
++
++metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc
++
++make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc
++
++test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc
++
++row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \
++ row_metadata_experiment.cc
++
++matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \
++ output_archive.hh timing.hh timing.cc matrix_benchmark.cc
++
++matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \
++ timing.hh timing.cc matrix_benchmark_write.cc
++
++matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \
++ timing.hh timing.cc matrix_benchmark_read.cc
++
++snpfile_genotype_count_SOURCES = genotype_count.cc
+
+ snpfileincludedir = $(includedir)/snpfile
+-snpfileinclude_HEADERS =
+-snpfileinclude_HEADERS += common.hh
+-snpfileinclude_HEADERS += matrix.hh
+-snpfileinclude_HEADERS += file_matrix.hh
+-snpfileinclude_HEADERS += array_matrix.hh
+-snpfileinclude_HEADERS += byte_order_handler.hh
+-snpfileinclude_HEADERS += metadata.hh
+-snpfileinclude_HEADERS += metadata_access.hh
+-snpfileinclude_HEADERS += archive_common.hh
+-snpfileinclude_HEADERS += archives.hh
+-snpfileinclude_HEADERS += input_archive.hh
+-snpfileinclude_HEADERS += output_archive.hh
+-snpfileinclude_HEADERS += snpfile.hh
+-snpfileinclude_HEADERS += serialization_trait.hh
+-snpfileinclude_HEADERS += type_trait.hh
+-snpfileinclude_HEADERS += iterators.hh
+-snpfileinclude_HEADERS += tabulate.hh
+-
+-libsnpfile_a_SOURCES =
+-libsnpfile_a_SOURCES += common.hh
+-libsnpfile_a_SOURCES += matrix.hh matrix.cc
+-libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc
+-libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh
+-libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh
+-libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh
+-libsnpfile_a_SOURCES += archive_common.hh
+-libsnpfile_a_SOURCES += archives.hh
+-libsnpfile_a_SOURCES += input_archive.hh
+-libsnpfile_a_SOURCES += output_archive.hh
+-libsnpfile_a_SOURCES += snpfile.hh snpfile.cc
+-libsnpfile_a_SOURCES += serialization_trait.hh
+-libsnpfile_a_SOURCES += type_trait.hh
+-
+-text2snpfile_SOURCES =
+-text2snpfile_SOURCES += text2snpfile.cc
+-text2snpfile_LDFLAGS =
+-text2snpfile_LDFLAGS += -L.
+-text2snpfile_LDADD =
+-text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-text2snpfile_LDADD += $(BOOST_SIGNALS_LIB)
+-text2snpfile_LDADD += -lsnpfile
+-
+-snpfile2text_SOURCES =
+-snpfile2text_SOURCES += snpfile2text.cc
+-snpfile2text_LDFLAGS =
+-snpfile2text_LDFLAGS += -L.
+-snpfile2text_LDADD =
+-snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile2text_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile2text_LDADD += -lsnpfile
+-
+-
+-snpfile2fastPHASE_SOURCES =
+-snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc
+-snpfile2fastPHASE_LDFLAGS =
+-snpfile2fastPHASE_LDFLAGS += -L.
+-snpfile2fastPHASE_LDADD =
+-snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile2fastPHASE_LDADD += -lsnpfile
+-
+-fastPHASE2snpfile_SOURCES =
+-fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc
+-fastPHASE2snpfile_LDFLAGS =
+-fastPHASE2snpfile_LDFLAGS += -L.
+-fastPHASE2snpfile_LDADD =
+-fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB)
+-fastPHASE2snpfile_LDADD += -lsnpfile
+-
+-
+-snpfile2haploview_SOURCES =
+-snpfile2haploview_SOURCES += snpfile2haploview.cc
+-snpfile2haploview_LDFLAGS =
+-snpfile2haploview_LDFLAGS += -L.
+-snpfile2haploview_LDADD =
+-snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile2haploview_LDADD += -lsnpfile
+-
+-
+-beagle_phase_snpfile_SOURCES =
+-beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc
+-beagle_phase_snpfile_LDFLAGS =
+-beagle_phase_snpfile_LDFLAGS += -L.
+-beagle_phase_snpfile_LDADD =
+-beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
+-beagle_phase_snpfile_LDADD += -lsnpfile
+-
+-snpfile_genotype_count_SOURCES =
+-snpfile_genotype_count_SOURCES += genotype_count.cc
+-snpfile_genotype_count_LDFLAGS =
+-snpfile_genotype_count_LDFLAGS += -L.
+-snpfile_genotype_count_LDADD =
+-snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_genotype_count_LDADD += -lsnpfile
+-
+-snpfile_phenotypes_SOURCES =
+-snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc
+-snpfile_phenotypes_LDFLAGS =
+-snpfile_phenotypes_LDFLAGS += -L.
+-snpfile_phenotypes_LDADD =
+-snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_phenotypes_LDADD += -lsnpfile
+-
+-snpfile_markers_SOURCES =
+-snpfile_markers_SOURCES += snpfile_markers.cc
+-snpfile_markers_LDFLAGS =
+-snpfile_markers_LDFLAGS += -L.
+-snpfile_markers_LDADD =
+-snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_markers_LDADD += -lsnpfile
+-
+-snpfile_metadata_info_SOURCES =
+-snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc
+-snpfile_metadata_info_LDFLAGS =
+-snpfile_metadata_info_LDFLAGS += -L.
+-snpfile_metadata_info_LDADD =
+-snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_metadata_info_LDADD += -lsnpfile
+-
+-snpfile_set_metadata_SOURCES =
+-snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc
+-snpfile_set_metadata_LDFLAGS =
+-snpfile_set_metadata_LDFLAGS += -L.
+-snpfile_set_metadata_LDADD =
+-snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_set_metadata_LDADD += -lsnpfile
+-
+-snpfile_get_metadata_SOURCES =
+-snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc
+-snpfile_get_metadata_LDFLAGS =
+-snpfile_get_metadata_LDFLAGS += -L.
+-snpfile_get_metadata_LDADD =
+-snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_get_metadata_LDADD += -lsnpfile
+-
+-snpfile_split_on_column_SOURCES =
+-snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc
+-snpfile_split_on_column_LDFLAGS =
+-snpfile_split_on_column_LDFLAGS += -L.
+-snpfile_split_on_column_LDADD =
+-snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+-snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB)
+-snpfile_split_on_column_LDADD += -lsnpfile
++snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \
++ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \
++ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \
++ type_trait.hh iterators.hh tabulate.hh
++
++libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \
++ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \
++ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \
++ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \
++ type_trait.hh
++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB)
++
+--- configure.in
++++ configure.in
+@@ -1,10 +1,11 @@
+ AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
++AC_CONFIG_MACRO_DIR([m4])
+ AM_CONFIG_HEADER(config.hh)
+
++LT_INIT
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+-AC_PROG_RANLIB
+
+ if test "x$prefix" != xNONE; then
+ thePREFIX=$prefix
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
new file mode 100644
index 000000000000..2211aa36c0ca
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
@@ -0,0 +1,23 @@
+ Makefile.am | 4 ++--
+ 1 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 06fd733..5805c48 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile
+ noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
+ matrix_benchmark_write matrix_benchmark_read
+
+-LDADD = $(top_builddir)/libsnpfile.la
++LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
+
+ matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
+
+@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix
+ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \
+ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \
+ type_trait.hh
+-libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB)
++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
+
diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/snpfile/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild
new file mode 100644
index 000000000000..b06f628fa020
--- /dev/null
+++ b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools eutils multilib
+
+DESCRIPTION="A library and API for manipulating large SNP datasets"
+HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/"
+SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="static-libs"
+KEYWORDS="amd64 x86"
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc44.patch \
+ "${FILESDIR}"/${P}-gentoo.diff \
+ "${FILESDIR}"/${P}-gold.patch
+ eautoreconf
+}
+
+src_configure() {
+ econf $(use_enable static-libs static)
+}
+
+src_install() {
+ default
+ use static-libs || rm "${D}"/usr/$(get_libdir)/lib${PN}.la
+}
diff --git a/sci-biology/snpfile/snpfile-2.0.1.ebuild b/sci-biology/snpfile/snpfile-2.0.1.ebuild
new file mode 100644
index 000000000000..6f57debb2930
--- /dev/null
+++ b/sci-biology/snpfile/snpfile-2.0.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+inherit eutils
+
+DESCRIPTION="A library and API for manipulating large SNP datasets"
+HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/"
+SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+RDEPEND="dev-libs/boost"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc44.patch
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+}
diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest
new file mode 100644
index 000000000000..cd6e1754804f
--- /dev/null
+++ b/sci-biology/stride/Manifest
@@ -0,0 +1,2 @@
+DIST stride-20060723-update.patch.bz2 5621 SHA256 8d48627c294b4efba67acba10fba47b20c0a8d5f7e06c2775a2d7eaaa0aa7b81 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1 WHIRLPOOL fbe19cd7da96a845a001f5fcfb6c0aed7b9c4c152b48ef9ab9df63b1d72c9a97e545c9a6e12c5c58823210dd48050392b0a9c0758c1d57c3677ac5092de863f9
+DIST stride.tar.gz 56441 SHA256 d272700bccd046199f6ea1faed31a2a2662a7d5f13b7663736a1818ac18c87b9 SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b WHIRLPOOL 843c789eda18da69a670a134f8a19103381ac86d611a3e1f0b47e17c3d171a195b8064d131ec3f81a561a65d8536d5f8a8c3a490776646b50ecb6aee36c46536
diff --git a/sci-biology/stride/files/stride-LDFLAGS.patch b/sci-biology/stride/files/stride-LDFLAGS.patch
new file mode 100644
index 000000000000..1761b12129bd
--- /dev/null
+++ b/sci-biology/stride/files/stride-LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- Makefile 2009-10-27 21:18:45.000000000 +0100
++++ Makefile.new 2009-10-27 21:19:00.000000000 +0100
+@@ -12,7 +12,7 @@
+
+
+ stride : $(OBJECT)
+- $(CC) $(OBJECT) $(FLAGS) $(BINDIR)/stride
++ $(CC) $(LDFLAGS) $(OBJECT) $(FLAGS) $(BINDIR)/stride
+
+ $(OBJECT) : stride.h protot.h
+
diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/stride/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
new file mode 100644
index 000000000000..0848427631a0
--- /dev/null
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Protein secondary structure assignment from atomic coordinates"
+HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/"
+SRC_URI="
+ ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz
+ http://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2"
+
+SLOT="0"
+LICENSE="STRIDE"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+S="${WORKDIR}"
+
+RESTRICT="mirror bindist"
+
+src_prepare() {
+ # this patch updates the source to the most recent
+ # version which was kindly provided by the author
+ epatch \
+ "${DISTDIR}/${PN}-20060723-update.patch.bz2" \
+ "${FILESDIR}"/${PN}-LDFLAGS.patch
+
+ # fix makefile
+ sed -e "/^CC/s|gcc -g|$(tc-getCC) ${CFLAGS}|" -i Makefile || \
+ die "Failed to fix Makefile"
+}
+
+src_install() {
+ dobin ${PN}
+}
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
new file mode 100644
index 000000000000..d7abf3e8ff7d
--- /dev/null
+++ b/sci-biology/t-coffee/Manifest
@@ -0,0 +1,2 @@
+DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 SHA256 b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 WHIRLPOOL 205eb1b416b38c4d86722ec501d815cc3f9f974a79e07f6fff32855972a9d3a9849585ca345fa66bbcbe15dca8f16930e7bafe44ce5d39e23f9f73023da13b7c
+DIST T-COFFEE_distribution_Version_9.03.r1318.tar.gz 3455629 SHA256 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c SHA512 40220c9fca5bee59b66757162ff2279c2ab221cca07532c64ed3606a95a787080cd4d6bf301ca6d20d8ba4f0c2166e5785fc0ad81ed6528eb527f24d59e79cc8 WHIRLPOOL a9d6b5abdf9851289d1de985fe0eda16f40d72ad23c74ee80ec7a365d9e6124ba12b4dc17894b98bd8d886f4dd0a25bce96cd4e2ec1bc7c2177d6ab8aa00bb65
diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch
new file mode 100644
index 000000000000..5b15108b3bfa
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch
@@ -0,0 +1,21 @@
+ t_coffee_source/makefile | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile
+index 9e01ba0..026b714 100644
+--- a/t_coffee_source/makefile
++++ b/t_coffee_source/makefile
+@@ -1,6 +1,6 @@
+
+ t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o
+- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm
++ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm
+
+ all: t_coffee TMalign
+
+@@ -8,4 +8,4 @@ clean:
+ rm *.o
+
+ TMalign:
+- $(FCC) TMalign.f -o TMalign
++ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
new file mode 100644
index 000000000000..9a577185ee36
--- /dev/null
+++ b/sci-biology/t-coffee/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ T-Coffee is a multiple sequence alignment package. Given a set of
+ sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+ alignment. Version 2.00 and higher can mix sequences and structures.
+ T-Coffee allows the combination of a collection of multiple/pairwise,
+ global or local alignments into a single model. It also allows to
+ estimate the level of consistency of each position within the new
+ alignment with the rest of the alignments.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/t-coffee/t-coffee-11.00.ebuild b/sci-biology/t-coffee/t-coffee-11.00.ebuild
new file mode 100644
index 000000000000..62e8b7033cbe
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-11.00.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_HASH="8cbe486"
+MY_PV="${PV}.${MY_HASH}"
+MY_P="T-COFFEE_distribution_Version_${MY_PV}"
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+ sci-biology/clustalw
+ sci-chemistry/tm-align"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed \
+ -e '/@/s:.*;:\t:g' \
+ -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
+ -i t_coffee_source/makefile || die
+}
+
+src_compile() {
+ [[ $(gcc-version) == "3.4" ]] || \
+ [[ $(gcc-version) == "4.1" ]] && \
+ append-flags -fno-unit-at-a-time
+ emake \
+ V=1 \
+ CC="$(tc-getCXX)" \
+ CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
+ -C t_coffee_source t_coffee
+}
+
+src_install() {
+ dobin t_coffee_source/t_coffee
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r example
+ fi
+}
diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
new file mode 100644
index 000000000000..4b56c05793b5
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator
+
+MY_PV="$(replace_version_separator 2 .r)"
+MY_P="T-COFFEE_distribution_Version_${MY_PV}"
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+ sci-biology/clustalw
+ sci-chemistry/tm-align"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+die_compile() {
+ echo
+ eerror "If you experience an internal compiler error (consult the above"
+ eerror "messages), try compiling t-coffee using very modest compiler flags."
+ eerror "See bug #114745 on the Gentoo Bugzilla for more details."
+ die "Compilation failed"
+}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-flags.patch
+}
+
+src_compile() {
+ [[ $(gcc-version) == "3.4" ]] || \
+ [[ $(gcc-version) == "4.1" ]] && \
+ append-flags -fno-unit-at-a-time
+ emake \
+ CC="$(tc-getCC)" \
+ CFLAGS="${CFLAGS}" \
+ -C t_coffee_source t_coffee
+}
+
+src_install() {
+ dobin t_coffee_source/t_coffee
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r example
+ fi
+}
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
new file mode 100644
index 000000000000..2d7d1928582d
--- /dev/null
+++ b/sci-biology/tophat/Manifest
@@ -0,0 +1,6 @@
+DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2
+DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937
+DIST tophat-2.0.0.tar.gz 1750811 SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 SHA512 5bd1dcc79c301dc0b464dd95d6da2b2ed69c4e003bc1f9c5cb556a7974bcdb86cbe6f7d8912856691ca89e9a5a10cbe10fa7391c4bbdc163408e1e57afed7295 WHIRLPOOL ace795553630bcd1e9966cae2ed2c42195dea2f3845fe778d591ad0214afef28ca389f32f0bd53ad01d1e3a520be140e77305313992be16259c111a9aa5e8514
+DIST tophat-2.0.2.tar.gz 1759933 SHA256 f9e40ae123dab24d2f2d6896ebf191c8ae3c05c80da6d4d965defe7579d553e0 SHA512 8341d406bfc2b86323932a151ad60469c6d50031bace433c5e3b6678a92eaed3516744fb9077d0e8944018275642050e2e9aca0126b4dd69423754c3dc9ae83c WHIRLPOOL 45a52fc96b258f4ae0b5b7a4d1dc4c22885e0b9230891dde1db85671deeceb3213008de02878cc3b1f9dc6af68b40bc897f691a1835bd4abf29d1a2bde42e1c2
+DIST tophat-2.0.8.tar.gz 1757036 SHA256 07d323d295effc99d4e261439c5ba2e10d5530af078e5de97c1a7bf1cbdd0da1 SHA512 c69360cc2f558c37d14b6a0e006f2483771ce5cdb42dc8397dd15a944a61d762843158adbf7c2bc89c2d4db46d9a02633dbd2721bf3376ef5d3ae6fb153db100 WHIRLPOOL a97ad6d47be23089605578a6f8ff9434afcb27a9fa58118b5b923af1d79530614af9fcaf5ebda2043603bf2dd8b10c2b7636e7b14662b9ab4f6e2059da4cb2b2
+DIST tophat-2.0.9.tar.gz 1766681 SHA256 9b506bbfdbb14b296d804557a50f41cc167480dfeed66a31c33e2ffb580afd38 SHA512 a81b801ee6c1f643d1fa507c2372d43ccdf4922d3f7ab76a34442c96aee78a3afc4a47ba164d46c6b6b6451aeae78b711c44c118e584da742940f74af7bc9610 WHIRLPOOL a67392251e592df62deb3fe58dcc4eadd0d0b1fe0a09389e48f1f30a7c591343794d1e1b2a27467c0a0f5a0e84dd5a5fbdef538a5bcf1b80ba8972e6ec02fbcf
diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
new file mode 100644
index 000000000000..ac1ca62da254
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.2-flags.patch
@@ -0,0 +1,124 @@
+ configure.ac | 6 +++---
+ src/Makefile.am | 30 +++++++++++++++---------------
+ 2 files changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 314a78e..f6933e6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++#generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
+@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim],
+ [if test "x$enable_optim" = xyes; then enable_optim=3; fi],
+ [enable_optim=3])
+
+-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])
++#AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])
+ AS_IF([test "x$enable_debug" = xyes],
+ [debug_CFLAGS="-DDEBUG"],
+ [debug_CFLAGS="-DNDEBUG"])
+@@ -92,7 +93,6 @@ AS_IF([test "x$enable_debug" = xyes],
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+ CXXFLAGS="$CFLAGS"
+ CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
+-LDFLAGS="$ext_LDFLAGS"
+
+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+
+diff --git a/src/Makefile.am b/src/Makefile.am
+index aa17841..42f9c0c 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -2,7 +2,7 @@
+
+ #SUBDIRS = samtools
+
+-#AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
++AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3
+
+ # Generated with
+ # find SeqAn-1.3 -type f -print | grep -v ".svn" | sed 's/$/ \\/g'
+@@ -550,7 +550,7 @@ CLEANFILES = \
+ tophat2
+
+ tophat2: tophat2.in
+- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
+
+ #SUFFIXES = .py
+ #.py:
+@@ -621,53 +621,53 @@ libgc_a_SOURCES = \
+ #-- program sources
+
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++prep_reads_LDADD = libtophat.a $(BAM_LIB)
+ prep_reads_LDFLAGS = $(BAM_LDFLAGS)
+
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ juncs_db_SOURCES = juncs_db.cpp
+-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++juncs_db_LDADD = libtophat.a $(BAM_LIB)
+ juncs_db_LDFLAGS = $(BAM_LDFLAGS)
+
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
+ fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam2fastx_SOURCES = bam2fastx.cpp
+-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
++bam2fastx_LDADD = libgc.a $(BAM_LIB)
+ bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam_merge_SOURCES = bam_merge.cpp
+-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ bam_merge_LDFLAGS = $(BAM_LDFLAGS)
+
+ closure_juncs_SOURCES = closures.cpp
+-closure_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++closure_juncs_LDADD = libtophat.a $(BAM_LIB)
+ closure_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++sam_juncs_LDADD = libtophat.a $(BAM_LIB)
+ sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ map2gtf_SOURCES = map2gtf.cpp
+-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ map2gtf_LDFLAGS = $(BAM_LDFLAGS)
+
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.8-flags.patch b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
new file mode 100644
index 000000000000..604f657d4c42
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.8-flags.patch
@@ -0,0 +1,105 @@
+ configure.ac | 3 ++-
+ src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
+ 2 files changed, 27 insertions(+), 26 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 75e9218..98b05d2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ user_LDFLAGS="$LDFLAGS"
+diff --git a/src/Makefile.am b/src/Makefile.am
+index dde692e..ebb9fcd 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -545,7 +545,7 @@ CLEANFILES = \
+ tophat2
+
+ tophat2: tophat2.in
+- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
+
+ #SUFFIXES = .py
+ #.py:
+@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
+ #-- program sources
+
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++prep_reads_LDADD = libtophat.a $(BAM_LIB)
++prep_reads_LDFLAGS = $(BAM_LDFLAGS)
+
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ juncs_db_SOURCES = juncs_db.cpp
+-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++juncs_db_LDADD = libtophat.a $(BAM_LIB)
++juncs_db_LDFLAGS = $(BAM_LDFLAGS)
+
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam2fastx_SOURCES = bam2fastx.cpp
+-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++bam2fastx_LDADD = libgc.a $(BAM_LIB)
++bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam_merge_SOURCES = bam_merge.cpp
+-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
++bam_merge_LDFLAGS = $(BAM_LDFLAGS)
+
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++sam_juncs_LDADD = libtophat.a $(BAM_LIB)
++sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ map2gtf_SOURCES = map2gtf.cpp
+-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
++map2gtf_LDFLAGS = $(BAM_LDFLAGS)
+
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
new file mode 100644
index 000000000000..af89e72084bf
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
@@ -0,0 +1,109 @@
+ configure.ac | 3 ++-
+ src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
+ 2 files changed, 27 insertions(+), 26 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 75e9218..98b05d2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
+ # set CFLAGS and CXXFLAGS
+ #user_CFLAGS="${CXXFLAGS}"
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
++generic_CFLAGS=""
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ user_LDFLAGS="$LDFLAGS"
+diff --git a/src/Makefile.am b/src/Makefile.am
+index dde692e..ebb9fcd 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -545,10 +545,10 @@ CLEANFILES = \
+ tophat2
+
+ tophat2: tophat2.in
+- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
+
+ tophat: tophat.py
+- sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
++ sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat
+
+ #SUFFIXES = .py
+ #.py:
+@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
+ #-- program sources
+
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++prep_reads_LDADD = libtophat.a $(BAM_LIB)
++prep_reads_LDFLAGS = $(BAM_LDFLAGS)
+
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ juncs_db_SOURCES = juncs_db.cpp
+-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++juncs_db_LDADD = libtophat.a $(BAM_LIB)
++juncs_db_LDFLAGS = $(BAM_LDFLAGS)
+
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam2fastx_SOURCES = bam2fastx.cpp
+-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++bam2fastx_LDADD = libgc.a $(BAM_LIB)
++bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
+
+ bam_merge_SOURCES = bam_merge.cpp
+-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
+-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
++bam_merge_LDFLAGS = $(BAM_LDFLAGS)
+
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
+-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++sam_juncs_LDADD = libtophat.a $(BAM_LIB)
++sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
+
+ map2gtf_SOURCES = map2gtf.cpp
+-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
++map2gtf_LDFLAGS = $(BAM_LDFLAGS)
+
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
+-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
new file mode 100644
index 000000000000..36cf4a138940
--- /dev/null
+++ b/sci-biology/tophat/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="bam">Compile support for the BAM format</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-1.0.12.ebuild b/sci-biology/tophat/tophat-1.0.12.ebuild
new file mode 100644
index 000000000000..88870c93982b
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.0.12.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit autotools
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="sci-biology/bowtie"
+
+src_prepare() {
+ # fix missing includes
+ sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die
+ sed -i \
+ -e '/#include <stdio.h>/ a #include <unistd.h>' \
+ "${S}/src/prep_reads.cpp" \
+ "${S}/src/extract_reads.cpp" || die
+ # fix parallel make race
+ sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die
+ # remove broken arch-dependent CFLAGS setting
+ perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die
+ eautoreconf
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS NEWS THANKS
+}
diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild
new file mode 100644
index 000000000000..3130c0d7c9c7
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.4.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic autotools
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="+bam"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+ sci-biology/bowtie"
+
+MAKEOPTS="${MAKEOPTS} -j1"
+
+src_prepare() {
+ filter-ldflags -Wl,--as-needed
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_with bam)
+}
diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild
new file mode 100644
index 000000000000..93159f65c773
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+bam debug"
+
+DEPEND="
+ dev-libs/boost
+ bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+ sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.0.2-flags.patch )
+
+src_configure() {
+ local myeconfargs=( $(use_enable debug) )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/tophat/tophat-2.0.2.ebuild b/sci-biology/tophat/tophat-2.0.2.ebuild
new file mode 100644
index 000000000000..7f68695af743
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+bam debug"
+
+DEPEND="
+ dev-libs/boost
+ bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+ sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_configure() {
+ local myeconfargs=( $(use_enable debug) )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
new file mode 100644
index 000000000000..c20007cd6160
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.8.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+ dev-libs/boost
+ sci-biology/samtools
+ sci-biology/seqan"
+RDEPEND="${DEPEND}
+ sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_prepare() {
+ rm -rf src/SeqAn* || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --disable-optim
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
new file mode 100644
index 000000000000..91cc2d463330
--- /dev/null
+++ b/sci-biology/tophat/tophat-2.0.9.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools-utils python-single-r1
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+ dev-libs/boost
+ sci-biology/samtools
+ sci-biology/seqan"
+RDEPEND="${DEPEND}
+ sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_prepare() {
+ rm -rf src/SeqAn* || die
+ autotools-utils_src_prepare
+}
+
+src_configure() {
+ local myeconfargs=(
+ --disable-optim
+ $(use_enable debug)
+ )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+ python_fix_shebang "${ED}"/usr/bin/tophat
+}
diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest
new file mode 100644
index 000000000000..d9522e5cccb5
--- /dev/null
+++ b/sci-biology/transfac/Manifest
@@ -0,0 +1 @@
+DIST transfac32.tar.Z 3346266 RMD160 892164634a80f388ba3c588823576ff0b5582338 SHA1 1f950c981364b03819463536c8d0195fe7351f02 SHA256 cf5c64e6f23037d73562d66f9dde56a767a8f31974a1c0906ec68edea3731a7f
diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml
new file mode 100644
index 000000000000..d07df4fd4dbf
--- /dev/null
+++ b/sci-biology/transfac/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ TRANSFAC® is a database of eukaryotic transcription factors, of their
+ genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old
+ public version available at the European Bioinformatics Institute.
+ TRANSFAC® is currently maintained by the BIOBASE company. Altough they
+ offer public access to a more recent version of the database, they
+ offer no free downloadable version.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/transfac/transfac-3.2.ebuild b/sci-biology/transfac/transfac-3.2.ebuild
new file mode 100644
index 000000000000..e2cdd68565f2
--- /dev/null
+++ b/sci-biology/transfac/transfac-3.2.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A database of eucaryotic transcription factors"
+HOMEPAGE="http://www.gene-regulation.com/pub/databases.html"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z"
+LICENSE="public-domain"
+
+SLOT="3"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="emboss minimal"
+# Minimal build keeps only the indexed files (if applicable) and the documentation.
+# The non-indexed database is not installed.
+
+DEPEND="emboss? ( sci-biology/emboss )"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_compile() {
+ if use emboss; then
+ echo
+ einfo "Indexing TRANSFAC for usage with EMBOSS."
+ EMBOSS_DATA=. tfextract -auto -infile class.dat || die \
+ "Indexing TRANSFAC failed."
+ echo
+ fi
+}
+
+src_install() {
+ if ! use minimal; then
+ insinto /usr/share/${PN}-${SLOT}
+ doins *.dat || die
+ fi
+ if use emboss; then
+ insinto /usr/share/EMBOSS/data
+ doins tf* || die
+ fi
+}
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
new file mode 100644
index 000000000000..4b855c8b51b8
--- /dev/null
+++ b/sci-biology/tree-puzzle/Manifest
@@ -0,0 +1 @@
+DIST tree-puzzle-5.2.tar.gz 875142 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751 WHIRLPOOL 145afdfc266809638d7b049beb65cdfc8fb6c108ecba831ba36fae938d58edd141fdf1762d9ce86269f0098043e7314b0ddefaa5e7f9b11cc6fd56a480b54d61
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
new file mode 100644
index 000000000000..93b960f5c2b4
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
@@ -0,0 +1,14 @@
+ src/sprng/primes-lcg64.c | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c
+index 8e5a7c9..fb04373 100644
+--- a/src/sprng/primes-lcg64.c
++++ b/src/sprng/primes-lcg64.c
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include "primes-lcg64.h"
+ #include "primelist-lcg64.h"
+
diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml
new file mode 100644
index 000000000000..cbdeede346fa
--- /dev/null
+++ b/sci-biology/tree-puzzle/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
+ from molecular sequence data by maximum likelihood. It implements a
+ fast tree search algorithm, quartet puzzling, that allows analysis of
+ large data sets and automatically assigns estimations of support to
+ each internal branch. TREE-PUZZLE also computes pairwise maximum
+ likelihood distances as well as branch lengths for user specified
+ trees. Branch lengths can be calculated under the clock-assumption. In
+ addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
+ investigate the support of a hypothesized internal branch without
+ computing an overall tree and to visualize the phylogenetic content of
+ a sequence alignment. TREE-PUZZLE also conducts a number of statistical
+ tests on the data set (chi-square test for homogeneity of base
+ composition, likelihood ratio clock test, Kishino-Hasegawa test). The
+ models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
+ nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
+ and F81 for two-state data. Rate heterogeneity is modeled by a discrete
+ Gamma distribution and by allowing invariable sites. The corresponding
+ parameters can be inferred from the data set.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
new file mode 100644
index 000000000000..fd2b06f1d159
--- /dev/null
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data"
+HOMEPAGE="http://www.tree-puzzle.de"
+SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="mpi"
+
+DEPEND="mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+pkg_setup () {
+ use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.
+ Either disable the \"mpi\" USE flag to compile only the non-parallelized
+ version of the program, or use gcc as your compiler (CC=\"gcc\")."
+}
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-impl-dec.patch
+}
+
+src_configure() {
+ default
+
+ if ! use mpi; then
+ sed \
+ -e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \
+ -e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \
+ -i "${S}"/src/Makefile || die
+ fi
+}
+
+src_install() {
+ dobin src/puzzle
+ use mpi && dobin src/ppuzzle
+ dodoc AUTHORS ChangeLog README
+
+ # User manual
+ insinto /usr/share/doc/${PF}
+ doins doc/tree-puzzle.pdf
+
+ # Example data files
+ insinto /usr/share/${PN}/data
+ rm data/Makefile*
+ doins data/*
+}
diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest
new file mode 100644
index 000000000000..024410ff1615
--- /dev/null
+++ b/sci-biology/treeviewx/Manifest
@@ -0,0 +1 @@
+DIST tv-0.5.1.tar.gz 426745 RMD160 27c92a0f43c59c8988fe2d1410adb6de429e94c9 SHA1 0b0887477ca0d9ded6d0ee8bef014b6208e1fc14 SHA256 118bdbefb3f21636b1ba9da92e1b2029cb4d7d9944f4d02d2deace4ebb14c2d1
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
new file mode 100644
index 000000000000..33bd3b1741f6
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
@@ -0,0 +1,77 @@
+diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp
+--- tv-0.5.1/TreeLib/Parse.cpp 2002-02-23 07:22:32.000000000 -0500
++++ tv-0.5.1.new/TreeLib/Parse.cpp 2008-06-17 06:08:24.000000000 -0400
+@@ -24,6 +24,11 @@
+ #include <ctype.h>
+ #include "Parse.h"
+
++
++
++
++#include <cstring>
++
+ // Return the next token in the string
+ tokentype Parser::NextToken ()
+ {
+diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp
+--- tv-0.5.1/TreeLib/TreeLib.cpp 2004-05-13 08:22:11.000000000 -0400
++++ tv-0.5.1.new/TreeLib/TreeLib.cpp 2008-06-17 05:58:17.000000000 -0400
+@@ -24,6 +24,8 @@
+ #include "TreeLib.h"
+ #include "Parse.h"
+
++
++#include <cstdlib>
+ #include <vector>
+
+
+diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp
+--- tv-0.5.1/TreeLib/treereader.cpp 2003-09-10 08:58:16.000000000 -0400
++++ tv-0.5.1.new/TreeLib/treereader.cpp 2008-06-17 06:07:15.000000000 -0400
+@@ -28,6 +28,9 @@
+ #include <stdlib.h>
+ #endif
+
++#include <cstring>
++#include <cstdlib>
++
+ //------------------------------------------------------------------------------
+ TreeReader::TreeReader (Tokeniser &p) : parser (p)
+ {
+diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp
+--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2002-12-10 06:35:49.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp 2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp
+--- tv-0.5.1/ncl-2.0/src/nexus.cpp 2002-12-10 06:35:50.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp 2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp
+--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2005-04-29 10:28:17.000000000 -0400
++++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp 2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp
+--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2001-02-02 07:55:40.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp 2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,6 @@
++
++#include <cstring>
++
+ #ifdef __BORLANDC__
+ // Undefine __MINMAX_DEFINED so that min and max are correctly defined
+ #ifdef __MINMAX_DEFINED
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch
new file mode 100644
index 000000000000..e3ba6b2fff50
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch
@@ -0,0 +1,14 @@
+Fix build w/ wxGTK-2.8
+http://bugs.debian.org/567238
+
+--- a/tview.cpp
++++ b/tview.cpp
+@@ -994,7 +994,7 @@ END_EVENT_TABLE()
+ MyCanvas::MyCanvas(wxView *v, wxMDIChildFrame *frame, const wxPoint& pos, const wxSize& size, long style):
+ wxScrolledWindow(frame, -1, pos, size, style)
+ {
+- SetBackgroundColour(wxColour("WHITE"));
++ SetBackgroundColour(wxColour(wxT("WHITE")));
+ view = v;
+ magnification = 1;
+ }
diff --git a/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch
new file mode 100644
index 000000000000..9d64fabb6a9b
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch
@@ -0,0 +1,73 @@
+--- TreeLib/nodeiterator.h.old 2002-02-24 15:37:17.000000000 -0500
++++ TreeLib/nodeiterator.h 2005-02-27 14:23:30.971981368 -0500
+@@ -128,34 +128,34 @@
+
+ template <class N> N *PreorderIterator<N>::begin ()
+ {
+- cur = root;
+- return cur;
++ this->cur = this->root;
++ return this->cur;
+ }
+
+ template <class N> N *PreorderIterator<N>::next ()
+ {
+- if (cur->GetChild())
++ if (this->cur->GetChild())
+ {
+- stk.push (cur);
+- N *p = (N *)(cur->GetChild());
+- cur = p;
++ this->stk.push (this->cur);
++ N *p = (N *)(this->cur->GetChild());
++ this->cur = p;
+ }
+ else
+ {
+- while (!stk.empty() && (cur->GetSibling() == NULL))
++ while (!this->stk.empty() && (this->cur->GetSibling() == NULL))
+ {
+- cur = stk.top();
+- stk.pop();
++ this->cur = this->stk.top();
++ this->stk.pop();
+ }
+- if (stk.empty())
+- cur = NULL;
++ if (this->stk.empty())
++ this->cur = NULL;
+ else
+ {
+- N *p = (N *)(cur->GetSibling());
+- cur = p;
++ N *p = (N *)(this->cur->GetSibling());
++ this->cur = p;
+ }
+ }
+- return cur;
++ return this->cur;
+ }
+
+
+--- TreeLib/profile.h.old 2002-12-10 06:37:57.000000000 -0500
++++ TreeLib/profile.h 2005-02-27 14:27:51.205419872 -0500
+@@ -77,7 +77,7 @@
+ #include <ctime>
+ #endif
+
+-
++using namespace std;
+
+ /**
+ *@typedef std::map <std::string, int, std::less<std::string> > LabelMap;
+--- TreeLib/treedrawer.cpp.old 2003-08-22 06:47:28.000000000 -0400
++++ TreeLib/treedrawer.cpp 2005-02-27 14:26:19.279394752 -0500
+@@ -406,7 +406,7 @@
+ if (q->IsLeaf())
+ {
+ double d = q->GetPathLength() - mMaxPathLength;
+- mUltrametric = (std::fabs(d) <= 0.0001);
++ mUltrametric = (fabs(d) <= 0.0001);
+ // cout << mMaxPathLength << ":" << q->GetPathLength() << " " << d << endl;
+ }
+ q = u.next();
diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch
new file mode 100644
index 000000000000..b1c03bbb39f9
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch
@@ -0,0 +1,50 @@
+--- tv.cpp~ 2005-10-01 16:47:35.000000000 -0400
++++ tv.cpp 2005-10-01 16:52:30.000000000 -0400
+@@ -312,11 +312,15 @@
+ {
+ #ifdef __WXMSW__
+ file_menu->AppendSeparator();
+- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile");
++ file_menu->Append(SAVEAS_PICTURE_CMD,
++ wxT("Save As Picture...")),
++ wxT("Save picture of tree to metafile");
+ #else
+ #ifdef USE_SVG
+ file_menu->AppendSeparator();
+- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file");
++ file_menu->Append(SAVEAS_PICTURE_CMD,
++ wxT("Save As Picture...")),
++ wxT("Save picture of tree to SVG file");
+ #endif
+ #endif
+ file_menu->AppendSeparator();
+--- tview.cpp~ 2005-10-01 16:47:45.000000000 -0400
++++ tview.cpp 2005-10-01 16:50:42.000000000 -0400
+@@ -184,10 +184,10 @@
+ wxString pictureFileName = GetFrame()->GetTitle();
+ pictureFileName += wxT(".emf");
+ wxFrame *f = GetMainFrame();
+- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+- "Enhanced metafile (*.emf)|*.emf",
+- wxSAVE|wxOVERWRITE_PROMPT);
+-
++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
++ pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"),
++ wxSAVE|wxOVERWRITE_PROMPT);
++
+ if (dialog.ShowModal() == wxID_OK)
+ {
+ wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ;
+@@ -204,9 +204,9 @@
+ #else
+ wxFrame *f = GetMainFrame();
+ #endif
+- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+- "SVG vector picture files (*.svg)|*.svg",
+- wxSAVE|wxOVERWRITE_PROMPT);
++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
++ pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"),
++ wxSAVE|wxOVERWRITE_PROMPT);
+
+ if (dialog.ShowModal() == wxID_OK)
+ {
diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml
new file mode 100644
index 000000000000..e351ff6c1fa9
--- /dev/null
+++ b/sci-biology/treeviewx/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ TreeView X is a program for displaying phylogenetic trees on Linux and
+ UNIX platforms. It can read and display NEXUS and Newick format tree
+ files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other
+ programs).
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild
new file mode 100644
index 000000000000..4ff83ca1f34c
--- /dev/null
+++ b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+WX_GTK_VER="2.8"
+inherit eutils wxwidgets
+
+DESCRIPTION="A phylogenetic tree viewer"
+HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/"
+SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz"
+LICENSE="GPL-2"
+
+KEYWORDS="amd64 x86"
+SLOT="0"
+IUSE=""
+
+DEPEND="x11-libs/wxGTK:2.8[X]"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/tv-${PV}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PN}-wxt.patch
+ epatch "${FILESDIR}"/${P}-gcc4.3.patch
+ epatch "${FILESDIR}"/${P}-wx28.patch
+}
+
+src_install() {
+ emake install DESTDIR="${D}" || die "make install failed"
+}
diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest
new file mode 100644
index 000000000000..621d293009ea
--- /dev/null
+++ b/sci-biology/trf/Manifest
@@ -0,0 +1 @@
+DIST trf404.linux 89853 SHA256 1b9e3917088684afc2287a078810858f7a8e50d90e7bad2d814d40dc24188058 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e WHIRLPOOL 7817c7eeb2c452ece7f71c2b7548fd9cda8c6796d5e77b2de46911f50bb271290b1a9601545efc50b94574c718e0e5e65d4a4e27f5cfd66c3590e9d5b7c5856c
diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/trf/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/trf/trf-4.04.ebuild b/sci-biology/trf/trf-4.04.ebuild
new file mode 100644
index 000000000000..81d540251f07
--- /dev/null
+++ b/sci-biology/trf/trf-4.04.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils
+
+MY_P="${PN}404"
+
+DESCRIPTION="Tandem Repeats Finder"
+HOMEPAGE="http://tandem.bu.edu/trf/trf.html"
+SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux"
+
+LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html
+SLOT="0"
+KEYWORDS="amd64 x86"
+RESTRICT="mirror bindist"
+
+S="${WORKDIR}"
+
+QA_PREBUILT="opt/${PN}/.*"
+
+src_unpack() {
+ cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die
+}
+
+src_install() {
+ exeinto /opt/${PN}
+ doexe trf404.linux.exe
+ dosym /opt/${PN}/${MY_P}.linux.exe /opt/bin/trf
+ # GTK version (http://tandem.bu.edu/trf/downloads/trf400.linuxgtk.exe) has broken linking
+ #if use gtk; then
+ # doexe trf400.linuxgtk.exe || die
+ # make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die
+ #fi
+}
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
new file mode 100644
index 000000000000..b82cf548c773
--- /dev/null
+++ b/sci-biology/trnascan-se/Manifest
@@ -0,0 +1,2 @@
+DIST trnascan-se-1.23.tar.bz2 482202 SHA256 a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a SHA512 4977febcecf8344fb77aad2eeb278637aebdb1d995fd26823e459b3767d4f40b20f57d343092cc2cb8024b0ccc385879f4b6406c69022f848aa1df0acf1a68d8 WHIRLPOOL 978328857eaef5666fcf38c22afabfb796984b5fa52a02a7167b653164ba0bc32fcb52d35159eef83732046245c598426739cd4ed63bf259ea85130dda17dd70
+DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
new file mode 100644
index 000000000000..e21da6e58db0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
@@ -0,0 +1,292 @@
+diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c
+--- trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.000000000 +0300
++++ trnascan-se-1.23/sqio.c 2009-08-05 21:45:53.000000000 +0300
+@@ -235,7 +235,7 @@
+ }
+
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ readline(V->f, V->sbuffer);
+ }
+@@ -306,7 +306,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ done = feof(V->f);
+ done |= (*endTest)(V->sbuffer, &addend);
+ if (addend || !done)
+@@ -332,7 +332,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -341,7 +341,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -350,7 +350,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -364,7 +364,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -382,7 +382,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -394,7 +394,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -416,7 +416,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -425,7 +425,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -443,7 +443,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -454,7 +454,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -487,11 +487,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -521,12 +521,12 @@
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+- getline(V); /*skip title-junk line*/
++ get_line(V); /*skip title-junk line*/
+
+ readLoop(0, endNBRF, V);
+
+ while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -559,7 +559,7 @@
+ } else Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -579,7 +579,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -625,7 +625,7 @@
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -652,7 +652,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -661,7 +661,7 @@
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -685,7 +685,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -701,7 +701,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -712,7 +712,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -734,7 +734,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -746,7 +746,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -754,7 +754,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -786,14 +786,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -801,7 +801,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -848,7 +848,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -862,7 +862,7 @@
+ SeqfilePosition(SQFILE *sqfp, long offset)
+ {
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -954,7 +954,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
new file mode 100644
index 000000000000..783e4340823d
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: $(PROGS) tRNAscanSE setpaths
+
+ covels-SE: $(OBJ) scan_main.o
+- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+
+ coves-SE: $(OBJ) score_main.o
+- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \
++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ pavesi.o $(SQUIDOBJ) $(LIBS)
+
+ trnascan-1.4: trnascan.o
+- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+
+ tRNAscanSE:
+ $(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
new file mode 100644
index 000000000000..f28b1e8f6bb0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: $(PROGS) tRNAscan-SE setpaths
+
+ covels-SE: $(OBJ) scan_main.o
+- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+
+ coves-SE: $(OBJ) score_main.o
+- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \
++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ pavesi.o $(SQUIDOBJ) $(LIBS)
+
+ trnascan-1.4: trnascan.o
+- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+
+ tRNAscan-SE:
+ $(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
new file mode 100644
index 000000000000..55de1683677f
--- /dev/null
+++ b/sci-biology/trnascan-se/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
+ genes, with a false positive rate of less than one per 15 gigabases,
+ and with a search speed of about 30 kb/second. It was implemented for
+ large-scale human genome sequence analysis, but is applicable to
+ other DNAs as well.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
new file mode 100644
index 000000000000..aa8abf707262
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+ epatch "${FILESDIR}"/${P}-ldflags.patch
+ sed -e "s%BINDIR = \$(HOME)/bin%BINDIR = ${EPREFIX}/usr/bin%" \
+ -e "s%LIBDIR = \$(HOME)/lib/tRNAscan-SE%LIBDIR = ${EPRFIX}/usr/$(get_libdir)/${PN}%" \
+ -e "s%MANDIR = \$(HOME)/man%MANDIR = ${EPREFIX}/usr/share/man%" \
+ -e "s%CC = gcc%CC = $(tc-getCC)%" \
+ -e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \
+ -i Makefile || die
+}
+
+src_install() {
+ mv tRNAscan-SE.man tRNAscan-SE.man.1 || die
+ dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die
+ doman tRNAscan-SE.man.1 || die
+ dodoc MANUAL README Release.history || die
+ insinto /usr/$(get_libdir)/${PN}/
+ doins *.cm gcode.* Dsignal TPCsignal || die
+ insinto /usr/share/doc/${PF}
+ doins Manual.ps || die
+}
+
+src_test() {
+ make PATH="${S}:${PATH}" testrun || die
+}
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
new file mode 100644
index 000000000000..aa9b3a03fd8f
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+
+inherit eutils perl-module toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-ldflags.patch
+ sed \
+ -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
+ -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \
+ -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \
+ -e "s:CC = gcc:CC = $(tc-getCC):" \
+ -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
+ -i Makefile || die
+
+ perl_set_version
+}
+
+src_test() {
+ emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+ dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+ newman tRNAscan-SE.man tRNAscan-SE.man.1
+
+ dodoc MANUAL README Release.history
+
+ insinto /usr/share/${PN}/
+ doins *.cm gcode.* Dsignal TPCsignal
+
+ dodoc Manual.ps
+
+ insinto ${VENDOR_LIB}
+ doins -r tRNAscanSE
+}
diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
new file mode 100644
index 000000000000..e17b1c93e220
--- /dev/null
+++ b/sci-biology/uchime/Manifest
@@ -0,0 +1 @@
+DIST uchime4.2.40_src.tar.gz 66772 SHA256 cb6a3aea4e8b4343a6e0ddde3b2755bbec53492bae5d6252ce8a7091061f353d SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b WHIRLPOOL 28ad19892ac8b4db03e93fd1fca39b05d6675c241a97f7a2ab241765589b34c56684ab4923eaf568a5f9b0e1583ce1460be7f0edf9d9201e5d3db3da0efb0ee6
diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt
new file mode 100644
index 000000000000..54b0a3ba0d30
--- /dev/null
+++ b/sci-biology/uchime/files/CMakeLists.txt
@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 2.6)
+project(UCHIME)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
+
+# Simply copy the source files from the mk script
+add_executable(uchime
+ addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp)
+
+INSTALL(TARGETS uchime
+ DESTINATION bin)
diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml
new file mode 100644
index 000000000000..a3c0f91c8a08
--- /dev/null
+++ b/sci-biology/uchime/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+UCHIME is a new algorithm for detecting chimeric sequences. It was developed in
+collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob
+Knight. Chimeras are commonly created during DNA sample amplification by
+PCR, especially in community sequencing experiments using single regions
+such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can
+detect chimeras using a reference database or de novo using abundance
+information on the assumption that chimeras are less abundant than their
+parents because they must have undergone fewer rounds of amplification.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild
new file mode 100644
index 000000000000..19b55f5039e4
--- /dev/null
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit cmake-utils
+
+MY_P="${PN}${PV}_src"
+
+DESCRIPTION="Fast, accurate chimera detection"
+HOMEPAGE="http://www.drive5.com/uchime/"
+SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt . || die
+}
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
new file mode 100644
index 000000000000..3cf6c6051f97
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -0,0 +1 @@
+DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
new file mode 100644
index 000000000000..f1f3ccfb77e0
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
new file mode 100644
index 000000000000..d897ce479df7
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs flag-o-matic webapp
+
+DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
+HOMEPAGE="http://genome.ucsc.edu/"
+SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
+
+LICENSE="blat"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+mysql +server static-libs"
+
+REQUIRED_USE="server? ( mysql )"
+
+WEBAPP_MANUAL_SLOT="yes"
+
+DEPEND="
+ app-arch/unzip
+ !<sci-biology/ucsc-genome-browser-223
+ mysql? ( virtual/mysql )
+ server? ( virtual/httpd-cgi )" # TODO: test with other webservers
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/kent"
+
+src_prepare() {
+ use server && webapp_src_preinst
+ sed \
+ -e 's/-Werror//' \
+ -e "/COPT/s:=.*$:=${LDFLAGS}:g" \
+ -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
+ -e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \
+ -i src/inc/common.mk src/hg/lib/makefile || die
+ find -name makefile -or -name cgi_build_rules.mk \
+ | xargs sed -i \
+ -e 's/-${USER}//g' \
+ -e 's/-$(USER)//g' \
+ -e 's:-O2::g' \
+ -e 's:-ggdb::g' \
+ -e 's:-pipe::g' || die
+ sed \
+ -e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \
+ -i src/hg/genePredToMafFrames/makefile || die
+}
+
+src_compile() {
+ export MACHTYPE=${MACHTYPE/-*/} \
+ BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \
+ SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \
+ ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \
+ PATH="${BINDIR}:${PATH}" \
+ STRIP="echo 'skipping strip' "
+
+ export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
+
+ use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+ MYSQLINC="${ROOT}usr/include/mysql"
+
+ use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
+ CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
+
+ mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
+ use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
+
+ emake -C src clean
+ emake -C src/lib
+ emake -C src/jkOwnLib
+ emake -C src/utils/stringify
+ emake -C src blatSuite
+ if use mysql; then
+ emake -j1 -C src/hg utils
+ emake -j1 -C src utils
+ emake -C src libs userApps
+ if use server; then
+ emake -j1 -C src/hg
+ emake -j1 -C src
+ fi
+ fi
+}
+
+src_install() {
+ use server && webapp_src_preinst
+ cp -ad "${WORKDIR}"/destdir/* "${D}" || die
+ use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a
+ echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}"
+ doenvd "${S}/98${PN}"
+
+ use server && webapp_postinst_txt en src/product/README.QuickStart
+ use server && webapp_src_install
+
+ insinto "/usr/include/${PN}"
+ doins src/inc/*.h
+ insinto "/usr/share/${PN}"
+ doins -r src/product
+ keepdir "/usr/share/doc/${PF}"
+ find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die
+}
+
+pkg_postinst() {
+ use server && webapp_pkg_postinst
+}
diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest
new file mode 100644
index 000000000000..c9d5717af552
--- /dev/null
+++ b/sci-biology/unafold/Manifest
@@ -0,0 +1 @@
+DIST unafold-3.8.tar.bz2 282418 SHA256 7552724ce82ad8618167ec0524d8c931ac4383314669322c8424cafc06c2bf38 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c WHIRLPOOL 9fd5744e66d8669817433b5427fc671ac5185760ffaf0682a7938fc5542f24cbe7b08f7722c7135cd3197af2d748740e0ca35a70a5f6c40a4a5d5aaa806ed923
diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/unafold/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild
new file mode 100644
index 000000000000..f47f9d02ab36
--- /dev/null
+++ b/sci-biology/unafold/unafold-3.8-r1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit flag-o-matic
+
+DESCRIPTION="Unified Nucleic Acid Folding and hybridization package"
+HOMEPAGE="http://mfold.rna.albany.edu/"
+SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2"
+
+LICENSE="unafold"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ # recommended in README
+ use custom-cflags || append-flags -O3
+
+ sed \
+ -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \
+ -i tests/hybrid.tml || die
+}
diff --git a/sci-biology/unafold/unafold-3.8.ebuild b/sci-biology/unafold/unafold-3.8.ebuild
new file mode 100644
index 000000000000..5d258f941645
--- /dev/null
+++ b/sci-biology/unafold/unafold-3.8.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit flag-o-matic
+
+DESCRIPTION="Unified Nucleic Acid Folding and hybridization package"
+HOMEPAGE="http://mfold.rna.albany.edu/"
+SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2"
+
+LICENSE="unafold"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ # recommended in README
+ append-flags -O3
+
+ sed \
+ -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \
+ -i tests/hybrid.tml || die
+}
+
+src_install() {
+ einstall || die
+}
diff --git a/sci-biology/update-blastdb/Manifest b/sci-biology/update-blastdb/Manifest
new file mode 100644
index 000000000000..5d5b09e31d1f
--- /dev/null
+++ b/sci-biology/update-blastdb/Manifest
@@ -0,0 +1 @@
+DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867
diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/update-blastdb/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild
new file mode 100644
index 000000000000..8dbd69344fff
--- /dev/null
+++ b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit versionator
+
+MY_PV="$(replace_all_version_separators _)"
+
+DESCRIPTION="update_blastdb.pl for local blast db maintainance"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-lang/perl
+ !sci-biology/ncbi-tools++"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_install() {
+ dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl
+}
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
new file mode 100644
index 000000000000..8276750cfdc6
--- /dev/null
+++ b/sci-biology/vaal/Manifest
@@ -0,0 +1,2 @@
+DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175
+DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f
diff --git a/sci-biology/vaal/files/vaal-1.2-as-needed.patch b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
new file mode 100644
index 000000000000..31649010dbe3
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
@@ -0,0 +1,22 @@
+--- VAAL.orig/MakeDepend.cc 2008-12-18 17:05:48.000000000 +0100
++++ VAAL/MakeDepend.cc 2010-02-14 13:42:23.734370178 +0100
+@@ -1195,9 +1195,6 @@
+ }
+ }
+ mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)";
+- for ( set<string>::iterator dep_iter = lib_deps.begin();
+- dep_iter != lib_deps.end(); ++dep_iter )
+- mf << " " << "$(" << *dep_iter << "_LFLAGS)";
+ for ( set<string>::iterator dep_iter = sharedlib_deps.begin();
+ dep_iter != sharedlib_deps.end(); ++dep_iter ) {
+ // Extract the symbolic name of this library from its filename.
+@@ -1208,6 +1205,9 @@
+ mf << " -l" << sharedlib_name;
+ }
+ mf << " -l" << libname;
++ for ( set<string>::iterator dep_iter = lib_deps.begin();
++ dep_iter != lib_deps.end(); ++dep_iter )
++ mf << " " << "$(" << *dep_iter << "_LFLAGS)";
+ mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
+ }
+ }
diff --git a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch
new file mode 100644
index 000000000000..c021fadb44b1
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch
@@ -0,0 +1,39 @@
+diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h
+--- VAAL.orig/SortKmersImpl.h 2009-11-12 13:02:40.116993289 +0000
++++ VAAL/SortKmersImpl.h 2009-11-12 13:04:59.416388534 +0000
+@@ -98,7 +98,7 @@
+ { if ( reads[l].size( ) < KSPAN ) continue;
+ unsigned int N = reads[l].size( ) - KSPAN + 1;
+ if ( S + 2*N >= R.size( ) ) {
+- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
+ if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" );
+ R.resize(nn);
+ }
+@@ -180,7 +180,7 @@
+ }
+ if ( q == N ) break;
+ if ( S + 2*N >= R.size( ) ) {
+- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
+ if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
+ R.resize(nn);
+ }
+@@ -207,7 +207,7 @@
+ top += Min( N - top, (unsigned int) 10000 );
+
+ if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) {
+- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
+ if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
+ R.resize(nn);
+ }
+@@ -318,7 +318,7 @@
+
+ top += Min( N - top, 10000 );
+ if ( S + 2*(top - q) >= R.size( ) ) {
+- unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) );
++ unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) );
+ if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" );
+ R.resize(nn);
+ }
diff --git a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
new file mode 100644
index 000000000000..d3420556b608
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
@@ -0,0 +1,60 @@
+--- VAAL.orig/Makefile.in 2009-04-02 21:43:42.000000000 +0200
++++ VAAL/Makefile.in 2010-02-14 14:20:26.222370302 +0100
+@@ -161,12 +161,16 @@
+ COMPILER = @CC@
+ CPLUSPLUS = @CXX@
+
++CFLAGS = @CFLAGS@
++CXXFLAGS = @CXXFLAGS@
++LDFLAGS = @LDFLAGS@
++
+ # QUIET=yes causes the compiler to be less verbose about warnings.
+ QUIET = no
+
+ # DEBUG=yes forces out-of-date executables to be built with symbolic
+ # debugging information. Any other value is ignored.
+-DEBUG = yes
++DEBUG = no
+
+ # OPTIM=<compiler optimization> forces user-defined optimizations to be used,
+ # rather than the compiler-specific default.
+@@ -174,7 +178,7 @@
+ # If OPTIM=none, then no optimization is used.
+ # If unset, defaults are used.
+ # -fno-exceptions
+-OPTIM =
++OPTIM = none
+
+ # PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other
+ # value is ignored.
+@@ -317,6 +321,7 @@
+ # Setup final compilation options:
+
+ CPP_OPTIONS = \
++ $(CXXFLAGS) \
+ $(SYS_WARN) \
+ $(SYS_OPT) \
+ $(SYS_DEBUG) \
+@@ -328,6 +333,7 @@
+ @INCLUDES@
+
+ LINK_OPTIONS = \
++ $(LDFLAGS) \
+ $(SYS_DEBUG) \
+ $(SYS_LINK) \
+ $(OMP_LINK) \
+@@ -406,12 +406,12 @@
+ $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
+
+ checkLock: $(SRC)/util/checkLock.cc
+- $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock
++ $(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock
+
+ random/Random.o: random/Random.cc
+ @ mkdir -p $(OBJ)/${@D}
+ cp $(SRC)/random/Random.cc $(SRC)/random/Random.c
+- $(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
++ $(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
+ rm $(SRC)/random/Random.c
+
+ MemTracker.o: MemTracker.cc
diff --git a/sci-biology/vaal/files/vaal-1.6-gcc47.patch b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
new file mode 100644
index 000000000000..0d80f08d3c21
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
@@ -0,0 +1,153 @@
+Fix building with gcc-4.7
+
+https://bugs.gentoo.org/show_bug.cgi?id=423497
+
+Patch written by Kacper Kowalik <xarthisius@gentoo.org>
+--- a/src/feudal/MasterVec.h
++++ b/src/feudal/MasterVec.h
+@@ -62,20 +62,20 @@
+ /// This function is deprecated: Use reserve() instead.
+ /// The pool size argument is ignored, anyway.
+ MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
+- { reserve(capacity); return *this; }
++ { this->reserve(capacity); return *this; }
+
+ /// This function is deprecated: Use clear().shrink_to_fit().
+ MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
+
+ /// This function is deprecated: Use push_back().
+ MasterVec& push_back_external( T const& val )
+- { push_back(val); return *this; }
++ { this->push_back(val); return *this; }
+
+ /// This function is deprecated: Use push_back().
+ MasterVec& push_back_reserve( T const& val,
+ size_type growthIncr = 0,
+ float growthFact = 1.3f )
+- { push_back(val,growthFact,growthIncr); return *this; }
++ { this->push_back(val,growthFact,growthIncr); return *this; }
+
+ /// This function is deprecated: Use append().
+ MasterVec& Append( MasterVec const& that )
+@@ -83,7 +83,7 @@
+
+ /// This function is deprecated: Use append().
+ MasterVec& Append( MasterVec const& that, size_type from, size_type to )
+- { append(that.begin(from),that.begin(to)); return *this; }
++ { this->append(that.begin(from),that.begin(to)); return *this; }
+
+ MasterVec const& WriteAll( String const& fileName ) const
+ { return WriteRange(fileName,0UL,BaseT::size()); return *this; }
+@@ -108,7 +108,7 @@
+ { if ( !append ) BaseT::clear();
+ FeudalFileReader rdr(fileName.c_str());
+ size_type siz = rdr.getNElements();
+- reserve(BaseT::size()+siz);
++ this->reserve(BaseT::size()+siz);
+ preAlloc(rdr,0,siz);
+ for ( size_type iii = 0; iii < siz; ++iii )
+ appendFromReader(rdr,iii);
+--- a/src/feudal/FeudalControlBlock.cc
++++ b/src/feudal/FeudalControlBlock.cc
+@@ -24,6 +24,7 @@
+ #include <string.h>
+ #include <errno.h>
+ #include <iostream>
++#include <unistd.h>
+
+ using std::cout;
+ using std::endl;
+--- a/src/feudal/SerfVec.h
++++ b/src/feudal/SerfVec.h
+@@ -83,9 +83,9 @@
+ { AssertLe(pos,that.size());
+ AssertLe(len,that.size()-pos);
+ if ( this != &that )
+- { assign(that.begin(pos),that.begin(pos+len)); }
++ { this->assign(that.begin(pos),that.begin(pos+len)); }
+ else
+- { erase(BaseT::begin(),BaseT::begin(pos));
++ { this->erase(BaseT::begin(),BaseT::begin(pos));
+ BaseT::resize(len); }
+ return *this; }
+
+--- a/src/system/ProcBuf.cc
++++ b/src/system/ProcBuf.cc
+@@ -195,12 +195,12 @@
+ Assert(M_internal_put_buffer == NULL);
+ M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
+ M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
+- setp(M_internal_put_buffer,
++ this->setp(M_internal_put_buffer,
+ M_internal_put_buffer_end);
+ } else if (!flush())
+ return traits_type::eof();
+ if (!traits_type::eq_int_type(c, traits_type::eof()))
+- return sputc(c);
++ return this->sputc(c);
+ else
+ return traits_type::not_eof(c);
+ }
+@@ -240,7 +240,7 @@
+ // (which is start of buffer)
+ std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
+ *(this->gptr()) = traits_type::to_char_type(c);
+- setg(this->eback(), this->gptr(), this->egptr()+1);
++ this->setg(this->eback(), this->gptr(), this->egptr()+1);
+ return traits_type::not_eof(c);
+ } else
+ return traits_type::eof();
+@@ -269,7 +269,7 @@
+ // doing wchars and we write an odd # of bytes?
+ return false;
+ } else {
+- setp(this->pbase(), this->epptr());
++ this->setp(this->pbase(), this->epptr());
+ return true;
+ }
+ }
+@@ -283,7 +283,7 @@
+ Assert(M_internal_get_buffer == NULL);
+ M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
+ M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
+- setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
++ this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
+ }
+ // The "get" pointer should be at the end of the buffer - that's
+ // why we need to fill it.
+@@ -318,7 +318,7 @@
+ //
+ // reset the get pointers
+ //
+- setg(M_internal_get_buffer,
++ this->setg(M_internal_get_buffer,
+ M_internal_get_buffer,
+ M_internal_get_buffer+numusable/sizeof(char_type));
+ return true;
+--- a/src/system/SysConf.cc
++++ b/src/system/SysConf.cc
+@@ -19,6 +19,7 @@
+ #include "system/SysConf.h"
+ #include "system/Exit.h"
+ #include <iostream>
++#include <unistd.h>
+
+ namespace
+ {
+--- a/src/Vec.h
++++ b/src/Vec.h
+@@ -261,11 +261,11 @@
+
+ template <class U>
+ void append( const vec<U>& y )
+- { insert( this->end( ), y.begin( ), y.end( ) ); }
++ { this->insert( this->end( ), y.begin( ), y.end( ) ); }
+
+ void append( const vec<T>& y, size_type i, size_type j ) {
+- if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
+- else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
++ if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
++ else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
+ }
+
+ // appends values in y, but only those whose indices are in entries
diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
new file mode 100644
index 000000000000..152fb423e924
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
@@ -0,0 +1,12 @@
+diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
+--- vaal-33805.orig/configure.ac 2010-09-20 04:37:49.858059826 +0000
++++ vaal-33805/configure.ac 2010-09-20 04:39:41.178059477 +0000
+@@ -14,7 +14,7 @@
+ AC_OPENMP
+ AC_OPENMP_CEHCK
+
+-CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
++CXXFLAGS+=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
+
+ OS_RELEASE="`uname -r`"
+ AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/vaal/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/vaal/vaal-46233.ebuild b/sci-biology/vaal/vaal-46233.ebuild
new file mode 100644
index 000000000000..6aee878ad2d1
--- /dev/null
+++ b/sci-biology/vaal/vaal-46233.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
+SRC_URI="
+ ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
+ ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+
+LICENSE="Whitehead-MIT"
+SLOT="0"
+KEYWORDS="amd64"
+IUSE="openmp"
+
+DEPEND=">=dev-libs/boost-1.41.0-r3"
+RDEPEND="${DEPEND}"
+
+DOCS=( "${DISTDIR}/VAAL_manual.doc" )
+
+src_prepare() {
+ sed \
+ -e '/COPYING/d' \
+ -i src/Makefile.am || die
+
+ sed \
+ -e 's:-ggdb::g' \
+ -e '/AC_OPENMP_CEHCK/d' \
+ -i configure.ac || die
+ autotools-utils_src_prepare
+}
+
+src_configure(){
+ local myeconfargs=( $(use_enable openmp) )
+ autotools-utils_src_configure
+}
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
new file mode 100644
index 000000000000..acbb2140b6da
--- /dev/null
+++ b/sci-biology/vcftools/Manifest
@@ -0,0 +1 @@
+DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863
diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
new file mode 100644
index 000000000000..85197664a0d1
--- /dev/null
+++ b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
@@ -0,0 +1,53 @@
+diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile
+--- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200
++++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200
+@@ -3,8 +3,8 @@
+ # ($Revision: 1.1 $)
+
+ # Compiler
+-CC = gcc
+-CPP = g++
++CC ?= gcc
++CPP ?= g++
+ # Output executable
+ EXECUTABLE = vcftools
+ # Flag used to turn on compilation of PCA routines
+@@ -12,9 +12,9 @@
+ VCFTOOLS_PCA = 0
+ endif
+ # Compiler flags
+-CFLAGS = -O2 -m64
++CFLAGS ?= -O2 -m64
+ #CFLAGS = -Wall -O2 -pg -m64
+-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64
++CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64
+ #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
+ # Included libraries (zlib)
+ LIB = -lz
+@@ -29,13 +29,13 @@
+ # Define flag for PCA routine compilation
+ CPPFLAGS += -DVCFTOOLS_PCA
+ # Add LAPACK library
+- LIB += -llapack
++ LIB += `$(PKG_CONFIG) --libs lapack`
+ # Add PCA source code
+ OBJS+= dgeev.o
+ endif
+
+ vcftools: $(OBJS)
+- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB)
+ ifdef BINDIR
+ cp $(CURDIR)/$@ $(BINDIR)/$@
+ endif
+@@ -47,8 +47,8 @@
+ -include $(OBJS:.o=.d)
+
+ %.o: %.cpp
+- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
+- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
++ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o
++ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d
+
+ # remove compilation products
+ clean:
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
new file mode 100644
index 000000000000..c45e9f4dea06
--- /dev/null
+++ b/sci-biology/vcftools/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">vcftools</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
new file mode 100644
index 000000000000..ddc214c430c0
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+ tc-export CXX PKG_CONFIG
+}
+
+src_compile() {
+ local myconf
+ use lapack && myconf="VCFTOOLS_PCA=1"
+ emake -C cpp ${myconf}
+}
+
+src_install(){
+ perl_set_version
+ dobin cpp/${PN}
+ insinto ${VENDOR_LIB}
+ doins perl/*.pm
+ dobin perl/{fill,vcf}-*
+ dodoc README.txt
+}
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
new file mode 100644
index 000000000000..08824f51b1cc
--- /dev/null
+++ b/sci-biology/velvet/Manifest
@@ -0,0 +1,2 @@
+DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad WHIRLPOOL 69dcb5a6760b66eba65d054562e873d2c000dc57b487cdcf2c977bc1c0106bf027a79ff3b7e81da8a0f82b00635b755c26135b34de51cae34f4d276f15c2be74
+DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64
diff --git a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
new file mode 100644
index 000000000000..883211a557d6
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff
@@ -0,0 +1,126 @@
+Debundle zlib, fixes parallel build, respect user FLAGS
+
+--- src/readSet.c
++++ src/readSet.c
+@@ -23,18 +23,13 @@
+ #include <string.h>
+ #include <math.h>
+ #include <time.h>
++#include <zlib.h>
+
+ #include "globals.h"
+ #include "tightString.h"
+ #include "readSet.h"
+ #include "utility.h"
+
+-#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+-#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+-#else
+-#include "../third-party/zlib-1.2.3/zlib.h"
+-#endif
+-
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+ # include <fcntl.h>
+ # include <io.h>
+
+--- Makefile
++++ Makefile
+@@ -1,77 +1,62 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
+-LDFLAGS = -lm
+-OPT = -O3
++LIBS = -lm -lz
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+
+-Z_LIB_DIR=third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
+-
+-# Mac OS users: uncomment the following lines
+-# Z_LIB_FILES=
+-# LDFLAGS = -lm -lz
+-# CFLAGS = -Wall -m64
+-
+-# Sparc/Solaris users: uncomment the following line
+-# CFLAGS = -Wall -m64
+-
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
++OBJDE = $(subst obj,objde,$(OBJ))
+
+-default : cleanobj zlib obj velveth velvetg doc
++default : cleanobj obj velveth velvetg
+
+ clean :
+- -rm obj/*.o obj/dbg/*.o ./velvet*
+- cd $(Z_LIB_DIR) && make clean
++ -rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o
+ -rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
+
+ cleanobj:
+- -rm obj/*.o obj/dbg/*.o
+-
+-zlib :
+- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++ -rm -f obj/*.o obj/dbg/*.o objde/*.o
+
+ velveth : obj
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(LIBS)
+
+
+ velvetg : obj
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(LIBS)
+
+ debug : cleanobj obj/dbg
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS)
+
+ color : cleanobj obj_de
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS)
++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS)
+
+ colordebug : cleanobj obj/dbg_de
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS)
+
+ objdir:
+ mkdir -p obj
++ mkdir -p objde
+
+-obj: zlib objdir $(OBJ)
++obj: objdir $(OBJ)
+
+-obj_de: override DEF := $(DEF) -D COLOR
+-obj_de: zlib cleanobj objdir $(OBJ)
++obj_de: cleanobj objdir $(OBJDE)
+
+ obj/dbgdir:
+ mkdir -p obj/dbg
+
+-obj/dbg: zlib obj/dbgdir $(OBJDBG)
++obj/dbg: obj/dbgdir $(OBJDBG)
+
+ obj/dbg_de: override DEF := $(DEF) -D COLOR
+-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
++obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG)
+
+ obj/%.o: src/%.c
+ $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
+
++objde/%.o: src/%.c
++ $(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@
++
+ obj/dbg/%.o: src/%.c
+ $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
+
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
new file mode 100644
index 000000000000..ed53a1229b5b
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
@@ -0,0 +1,72 @@
+diff -durr Makefile Makefile
+--- Makefile 2011-01-27 16:52:58.853408562 +0000
++++ Makefile 2011-01-27 17:01:45.088065521 +0000
+@@ -1,8 +1,4 @@
+-CC = gcc
+-CFLAGS = -Wall
+-DEBUG = -g
+-LDFLAGS = -lm
+-OPT = -O3
++LIBS = -lm -lz
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+@@ -41,29 +37,29 @@
+ -rm obj/*.o obj/dbg/*.o
+
+ zlib :
+- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++ echo "unbundled zlib"
+
+ velveth : obj
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS)
+
+
+ velvetg : obj
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
+
+ debug : override DEF := $(DEF) -D DEBUG
+ debug : cleanobj obj/dbg
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS)
+
+ color : override DEF := $(DEF) -D COLOR
+ color : cleanobj obj_de
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
+
+ colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
+ colordebug : cleanobj obj/dbg_de
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
+- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS)
++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS)
+
+ objdir:
+ mkdir -p obj
+@@ -83,7 +79,7 @@
+ obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
+
+ obj/%.o: src/%.c
+- $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
++ $(CC) $(CFLAGS) $(DEF) -c $? -o $@
+
+ obj/dbg/%.o: src/%.c
+ $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
+diff -durr src/readSet.c src/readSet.c
+--- src/readSet.c 2011-01-27 16:52:58.804084948 +0000
++++ src/readSet.c 2011-01-27 17:02:55.380324786 +0000
+@@ -24,6 +24,7 @@
+ #include <math.h>
+ #include <time.h>
+ #include <limits.h>
++#include <zlib.h>
+
+ #include "globals.h"
+ #include "tightString.h"
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/velvet/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
new file mode 100644
index 000000000000..c0bfb929033e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs flag-o-matic
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="-doc"
+KEYWORDS="amd64 x86"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}
+ doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+ # necessary?
+ # append-flags -O3 # as recommended by upstream
+ epatch "${FILESDIR}"/${P}-gentoo-r1.diff
+ use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+}
+
+src_compile() {
+ tc-export CC
+ MAKE_XOPTS=""
+ if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
+ if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
+ emake -j1 $MAKE_XOPTS || die
+ emake -j1 $MAKE_XOPTS color || die
+}
+
+src_install() {
+ dobin velvet{g,h,g_de,h_de} || die
+ insinto /usr/share/${PN}
+ doins -r contrib || die
+ dodoc Manual.pdf CREDITS.txt ChangeLog || die
+}
+
+pkg_postinst() {
+ elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+ elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+ elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+ elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+}
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
new file mode 100644
index 000000000000..86b06ffcd125
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+ doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+ if ! use doc; then
+ sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+ fi
+ elog "Upstream recommendes using -O3 in CFLAGS"
+ echo
+ elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+ elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+ elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+ elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+ MAKEOPTS+=" -j1"
+
+ if [[ $(tc-getCC) =~ gcc ]]; then
+ local eopenmp=-fopenmp
+ elif [[ $(tc-getCC) =~ icc ]]; then
+ local eopenmp=-openmp
+ else
+ elog "Cannot detect compiler type so not setting openmp support"
+ fi
+ append-flags -fPIC ${eopenmp}
+ append-ldflags ${eopenmp}
+
+ tc-export CC
+
+ MAKE_XOPTS=(
+ CC=$(tc-getCC)
+ CFLAGS="${CFLAGS}"
+ OPT="${CFLAGS}"
+ )
+ if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
+ if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
+}
+
+src_compile() {
+ emake "${MAKE_XOPTS[@]}"
+ emake "${MAKE_XOPTS[@]}" color
+}
+
+src_test() {
+ emake "${MAKE_XOPTS[@]}" test
+}
+
+src_install() {
+ dobin velvet{g,h,g_de,h_de}
+ insinto /usr/share/${PN}
+ doins -r contrib
+ dodoc Manual.pdf CREDITS.txt ChangeLog
+}
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
new file mode 100644
index 000000000000..d53e2f5d3ab7
--- /dev/null
+++ b/sci-biology/vienna-rna/Manifest
@@ -0,0 +1,2 @@
+DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f
+DIST ViennaRNA-2.1.8.tar.gz 5464683 SHA256 37a0a0b7c8a167bcdab1a85d88bcb1025ad8e00a4b00a147bf36d45dc8ca7560 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e WHIRLPOOL a79f30d49c9bbe047d9fe83054dc08e94535f17417ef1f412bbcdd374d1988a8f2faf679e154c1ed1d1a75799e6cc0232d30b3adf65b3fa19978322f67ace57e
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
new file mode 100644
index 000000000000..0a781667c70b
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
@@ -0,0 +1,22 @@
+diff -Naur ViennaRNA-1.6.5/Cluster/statgeom.c ViennaRNA-1.6.5.new/Cluster/statgeom.c
+--- ViennaRNA-1.6.5/Cluster/statgeom.c 2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.6.5.new/Cluster/statgeom.c 2007-11-24 08:55:17.000000000 -0500
+@@ -5,6 +5,7 @@
+ */
+
+ #include <stdio.h>
++#include <string.h>
+ #include <strings.h>
+ #include <ctype.h>
+ #include "utils.h"
+diff -Naur ViennaRNA-1.6.5/Readseq/readseq.c ViennaRNA-1.6.5.new/Readseq/readseq.c
+--- ViennaRNA-1.6.5/Readseq/readseq.c 1995-07-12 13:05:58.000000000 -0400
++++ ViennaRNA-1.6.5.new/Readseq/readseq.c 2007-11-24 08:56:16.000000000 -0500
+@@ -173,6 +173,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+
+ #include "ureadseq.h"
+
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
new file mode 100644
index 000000000000..37e2f8c6a880
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
@@ -0,0 +1,24 @@
+diff -Naur ViennaRNA-1.7.2/Perl/Makefile.am ViennaRNA-1.7.2.new/Perl/Makefile.am
+--- ViennaRNA-1.7.2/Perl/Makefile.am 2007-12-19 05:33:14.000000000 -0500
++++ ViennaRNA-1.7.2.new/Perl/Makefile.am 2008-10-06 14:20:54.000000000 -0400
+@@ -4,7 +4,7 @@
+ RNA.i tmaps.i
+
+ Makefile.perl: Makefile.PL Makefile
+- @PerlCmd@ Makefile.PL
++ @PerlCmd@ Makefile.PL LDDLFLAGS="${LDFLAGS} -shared"
+
+ # the perl command repairs some errors in the SWIG CVS version
+ RNA_wrap.c: RNA.i tmaps.i
+diff -Naur ViennaRNA-1.7.2/Readseq/Makefile ViennaRNA-1.7.2.new/Readseq/Makefile
+--- ViennaRNA-1.7.2/Readseq/Makefile 2008-01-23 05:32:00.000000000 -0500
++++ ViennaRNA-1.7.2.new/Readseq/Makefile 2008-10-06 14:21:13.000000000 -0400
+@@ -40,7 +40,7 @@
+
+ build: $(SOURCES)
+ @echo "Compiling readseq..."
+- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
+
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
new file mode 100644
index 000000000000..2c5ac3041297
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
@@ -0,0 +1,16 @@
+# unfortunately, vienna-rna's build system is a little broken and sometimes detects
+# gd in RNAforested but then realizes in g2 that it can't actually build it
+# resulting in unresolved symbols.
+
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in
+--- ViennaRNA-1.8.3.orig/RNAforester/configure.in 2009-09-10 13:05:40.507932827 +0000
++++ ViennaRNA-1.8.3/RNAforester/configure.in 2009-09-10 13:06:15.171952984 +0000
+@@ -47,7 +47,7 @@
+ save_CPPFLAGS=$CPPFLAGS
+ CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"]
+
+-AC_CHECK_LIB(gd,main,,)
++dnl AC_CHECK_LIB(gd,main,,)
+
+ dnl Checks for header files.
+ AC_HEADER_STDC
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
new file mode 100644
index 000000000000..025822f45c91
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
@@ -0,0 +1,76 @@
+diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c
+--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c 2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/AS_main.c 2009-09-10 11:58:32.915952366 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c
+--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c 2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/statgeom.c 2009-09-10 11:58:53.192452141 +0000
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <strings.h>
++#include <stdlib.h>
+ #include <ctype.h>
+ #include "utils.h"
+ #include "PS3D.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c
+--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c 2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/treeplot.c 2009-09-10 11:59:22.457509165 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include <math.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp
+--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp 2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp 2009-09-10 12:00:37.693252890 +0000
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+
+ //#include <sys/timeb.h>
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h 2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h 2009-09-10 12:01:41.631932654 +0000
+@@ -16,6 +16,7 @@
+
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+
+ #include "misc.h"
+ #include "types.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h 2009-09-10 11:56:01.620703294 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h 2009-09-10 12:02:29.687952726 +0000
+@@ -4,6 +4,7 @@
+ #include <assert.h>
+ #include <algorithm>
+ #include <climits>
++#include <cstring>
+
+ #include "algebra.h"
+ #include "debug.h"
+diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c
+--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c 2009-09-10 11:56:01.632743452 +0000
++++ ViennaRNA-1.8.3/Readseq/ureadseq.c 2009-09-10 12:03:15.343952776 +0000
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
++#include <stdlib.h>
+
+ #define UREADSEQ_G
+ #include "ureadseq.h"
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch
new file mode 100644
index 000000000000..76a5a259a862
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt
+
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
new file mode 100644
index 000000000000..c3f5b52141e8
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
@@ -0,0 +1,47 @@
+Fix implicit function declarations and attempt to free non-heap obj
+
+--- lib/subopt.c
++++ lib/subopt.c
+@@ -80,12 +80,12 @@
+ #include <string.h>
+ #include <math.h>
+ #include "fold.h"
++#include "cofold.h"
+ #include "utils.h"
+ #include "energy_par.h"
+ #include "fold_vars.h"
+ #include "pair_mat.h"
+ #include "list.h"
+-#include "subopt.h"
+ #include "params.h"
+
+ #define true 1
+--- Progs/RNAfold.c
++++ Progs/RNAfold.c
+@@ -20,6 +20,7 @@
+ #include "MEA.h"
+ extern void read_parameter_file(const char fname[]);
+ extern plist * stackProb(double cutoff);
++extern void init_pf_circ_fold(int length);
+
+ /*@unused@*/
+ static char UNUSED rcsid[] = "$Id$";
+--- Cluster/AS_main.c
++++ Cluster/AS_main.c
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <stdlib.h>
++#include <unistd.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+@@ -226,7 +227,7 @@
+ for(j=0;j<nn[i];j++) free(ss[i][j]);
+ free(ss[i]);
+ }
+- free(ss);
++ // free(ss); // attempt to free a non-heap object ‘ss’
+ }
+ else {
+ printf_taxa_list();
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch
new file mode 100644
index 000000000000..cfadc70bc6f6
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch
@@ -0,0 +1,18 @@
+diff -ur ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in
+--- ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in 2009-10-13 13:44:40.000000000 +0200
++++ ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in 2010-03-27 21:39:21.000000000 +0100
+@@ -116,12 +116,12 @@
+
+
+ clean:
+- -(cd ./demo ; make clean)
++ -(cd ./demo ; $(MAKE) clean)
+ -rm -f $(OBJ)
+ -rm -f libg2.a config.cache config.log Makefile.bak config.status
+ -rm -f ./include/*.h
+ -$(FIND) . -name "*~" -exec rm -f {} \;
+- -(cd ./g2_perl ; make clean)
++ -(cd ./g2_perl ; $(MAKE) clean)
+ -rm -f ./g2_perl/test.ps
+ -rm -f ./g2_perl/test.png
+ -rm -f ./g2_perl/test.jpg
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch
new file mode 100644
index 000000000000..fcaa5f9a53b6
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch
@@ -0,0 +1,26 @@
+Fix buffer overflows
+
+http://bugs.gentoo.org/show_bug.cgi?id=341089
+
+--- Readseq/ureadseq.c
++++ Readseq/ureadseq.c
+@@ -1579,7 +1579,7 @@
+
+ short linesout = 0, seqtype = kNucleic;
+ long i, j, l, l1, ibase;
+- char idword[31], endstr[10];
++ char idword[31], endstr[15];
+ char seqnamestore[128], *seqname = seqnamestore;
+ char s[kMaxseqwidth], *cp;
+ char nameform[10], numform[10], nocountsymbols[10];
+--- lib/part_func_up.c
++++ lib/part_func_up.c
+@@ -1438,7 +1438,7 @@
+ PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) {
+ int size,s,i,len;
+ double dG_u;
+- char nan[4], *time, startl[2], dg[10];;
++ char nan[4], *time, startl[3], dg[10];;
+ FILE *wastl;
+
+ wastl = fopen(ofile,"a");
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py
new file mode 100644
index 000000000000..0aeaf2a116d3
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+ os.rename(old_filename, new_filename)
+
+extra_link_args = []
+
+extension = Extension("_RNA",
+ ["Perl/RNA_wrap.c"],
+ libraries=['RNA'],
+ library_dirs=['lib'],
+ extra_link_args=extra_link_args
+ )
+
+setup(name="RNA",
+ version="1.8.5",
+ description="Vienna RNA",
+ author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+ url="http://www.tbi.univie.ac.at/RNA/",
+ package_dir = {'RNA':'Perl'},
+ packages = ['RNA'],
+ ext_modules=[extension],
+ )
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
new file mode 100644
index 000000000000..6d35ecea9b0f
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt
+
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
new file mode 100644
index 000000000000..de457f318e8e
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
@@ -0,0 +1,15 @@
+ Readseq/readseq.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/Readseq/readseq.c b/Readseq/readseq.c
+index 8af7b39..56a25ae 100644
+--- a/Readseq/readseq.c
++++ b/Readseq/readseq.c
+@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS '
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+
+ #include "ureadseq.h"
+
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
new file mode 100644
index 000000000000..ee4aef5c3308
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
@@ -0,0 +1,30 @@
+ Readseq/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Readseq/Makefile b/Readseq/Makefile
+index f073aaa..05f2edd 100644
+--- a/Readseq/Makefile
++++ b/Readseq/Makefile
+@@ -6,11 +6,11 @@
+ #
+
+ # pick an ANSI C compiler (the default Sun CC is not ANSI)
+-CC=gcc # Gnu C Compiler
++CC?=gcc # Gnu C Compiler
+ #CC=cc # SGI Irix
+ #CC=vcc # some DEC Ultrix
+
+-CFLAGS=
++CFLAGS?=
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+
+@@ -40,7 +40,7 @@ all: build test
+
+ build: $(SOURCES)
+ @echo "Compiling readseq..."
+- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
+
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
new file mode 100644
index 000000000000..57f6b712ba3d
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+ os.rename(old_filename, new_filename)
+
+extra_link_args = []
+
+extension = Extension("_RNA",
+ ["Perl/RNA_wrap.c"],
+ libraries=['RNA'],
+ library_dirs=['lib'],
+ extra_link_args=extra_link_args
+ )
+
+setup(name="RNA",
+ version="2.1.1",
+ description="Vienna RNA",
+ author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+ url="http://www.tbi.univie.ac.at/RNA/",
+ package_dir = {'RNA':'Perl'},
+ packages = ['RNA'],
+ ext_modules=[extension],
+ )
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
new file mode 100644
index 000000000000..e54dff95b485
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt ct2db
+
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
new file mode 100644
index 000000000000..50f4e02d4a18
--- /dev/null
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ The Vienna RNA Package consists of a C code library and several
+ stand-alone programs for the prediction and comparison of RNA secondary
+ structures. RNA secondary structure prediction through energy
+ minimization is the most used function in the package. We provide three
+ kinds of dynamic programming algorithms for structure prediction: the
+ minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
+ single optimal structure, the partition function algorithm of
+ (McCaskill 1990) which calculates base pair probabilities in the
+ thermodynamic ensemble, and the suboptimal folding algorithm of
+ (Wuchty et.al 1999) which generates all suboptimal structures within a
+ given energy range of the optimal energy. For secondary structure
+ comparison, the package contains several measures of distance
+ (dissimilarities) using either string alignment or tree-editing
+ (Shapiro and Zhang 1990). Finally, we provide an algorithm to design
+ sequences with a predefined structure (inverse folding).
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
new file mode 100644
index 000000000000..df5c8eb50f90
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="amd64 ppc x86"
+IUSE="doc openmp python static-libs"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+DEPEND="
+ dev-lang/perl
+ media-libs/gd
+ doc? ( dev-texlive/texlive-latex )
+ python? (
+ ${PYTHON_DEPS}
+ dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-bindir.patch
+ "${FILESDIR}"/${P}-prll.patch
+ "${FILESDIR}"/${P}-impl-decl.patch
+)
+
+src_prepare() {
+ sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+ sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
+
+ autotools-utils_src_prepare
+
+ if use python; then
+ cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
+ PATCHES=()
+ distutils-r1_src_prepare
+ fi
+}
+
+src_configure() {
+ local myeconfargs=(
+ --with-cluster
+ $(use_enable openmp) )
+
+ use doc || \
+ myeconfargs+=(
+ --without-doc-pdf
+ --without-doc-html
+ --without-doc
+ )
+ autotools-utils_src_configure
+ sed \
+ -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+ -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+ -i RNAforester/g2-0.70/Makefile || die
+ sed \
+ -e "s:CC=gcc:CC=$(tc-getCC):" \
+ -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+ -i Readseq/Makefile || die
+ use python && distutils-r1_src_configure
+}
+
+src_compile() {
+ autotools-utils_src_compile
+ autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+ # TODO: Add (optional?) support for the NCBI toolkit.
+ if use python; then
+ pushd Perl > /dev/null
+ mv RNA_wrap.c{,-perl} || die
+ swig -python RNA.i || die
+ popd > /dev/null
+ distutils-r1_src_compile
+ mv Perl/RNA_wrap.c{-perl,} || die
+ fi
+}
+
+src_test() {
+ autotools-utils_src_compile -C Perl check
+ autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ if ! use static-libs; then
+ rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+ fi
+
+ newbin Readseq/readseq readseq-vienna
+ dodoc Readseq/Readseq.help
+ newdoc Readseq/Readme README.readseq
+ newdoc Readseq/Formats Formats.readseq
+
+ # remove perlocal.pod to avoid file collisions (see #240358)
+ perl_delete_localpod || die "Failed to remove perlocal.pod"
+ use python && distutils-r1_src_install
+}
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
new file mode 100644
index 000000000000..8b862403e25f
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="doc openmp python static-libs"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+DEPEND="
+ dev-lang/perl
+ media-libs/gd
+ doc? ( dev-texlive/texlive-latex )
+ python? (
+ ${PYTHON_DEPS}
+ dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-bindir.patch
+ "${FILESDIR}"/${PN}-2.1.1-prll.patch
+ "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch
+)
+
+src_prepare() {
+ sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+ sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die
+
+ autotools-utils_src_prepare
+
+ if use python; then
+ cd interfaces/Python || die
+ local PATCHES=()
+ distutils-r1_src_prepare
+ fi
+}
+
+src_configure() {
+ local myeconfargs=(
+ --with-cluster
+ $(use_enable openmp)
+ )
+
+ use doc || \
+ myeconfargs+=(
+ --without-doc-pdf
+ --without-doc-html
+ --without-doc
+ )
+ autotools-utils_src_configure
+ sed \
+ -e "s:CC=gcc:CC=$(tc-getCC):" \
+ -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+ -i Readseq/Makefile || die
+ if use python; then
+ cd interfaces/Python || die
+ distutils-r1_src_configure
+ fi
+}
+
+src_compile() {
+ autotools-utils_src_compile
+ autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+ # TODO: Add (optional?) support for the NCBI toolkit.
+ if use python; then
+ cd interfaces/Python || die
+ emake RNA_wrap.c
+ distutils-r1_src_compile
+ fi
+}
+
+src_test() {
+ autotools-utils_src_compile -C interfaces/Perl check
+ use python && autotools-utils_src_compile -C interfaces/Python check
+ autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ if ! use static-libs; then
+ rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+ fi
+
+ newbin Readseq/readseq readseq-vienna
+ dodoc Readseq/Readseq.help
+ newdoc Readseq/Readme README.readseq
+ newdoc Readseq/Formats Formats.readseq
+
+ # remove perlocal.pod to avoid file collisions (see #240358)
+ perl_delete_localpod || die "Failed to remove perlocal.pod"
+ if use python; then
+ cd interfaces/Python || die
+ distutils-r1_src_install
+ fi
+}
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
new file mode 100644
index 000000000000..8a178bca08c9
--- /dev/null
+++ b/sci-biology/wgs-assembler/Manifest
@@ -0,0 +1,3 @@
+DIST wgs-5.4.tar.bz2 1876180 SHA256 698b22bd63fa2bb4fe7f164a92c92f82474bc8fc64c37704258ebb3bdc86d7bf
+DIST wgs-6.1.tar.bz2 1900084 SHA256 e00c1b64e857ea01f7e9a9f115dd91e290a380ccda217dd6a386f57754a3cff8 SHA512 3a9cfff43967bf28f557c71b387b3ca8fd56dcdaf15fa0cd1d4b845b7b4d006e8f2692b2097d281925d59bbc41eaac1c789b6993877cffd0e233a5a9050af83c WHIRLPOOL 88e9a3f85ddee01a8a17e989248857bb6483fbde59ce211986f64d8729e82174b6fc04b2f771eb1fc131706a6adb9710c75fb90be3923db8bce6387764e3fa03
+DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b
diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
new file mode 100644
index 000000000000..f7fb44743968
--- /dev/null
+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch
@@ -0,0 +1,229 @@
+ kmer/Make.rules | 4 ++--
+ kmer/configure.sh | 20 +++++++++----------
+ src/c_make.as | 58 +++++++++++++++++++++++++++----------------------------
+ src/c_make.gen | 4 ++--
+ 4 files changed, 43 insertions(+), 43 deletions(-)
+
+diff --git a/kmer/Make.rules b/kmer/Make.rules
+index f904b13..5c2d477 100644
+--- a/kmer/Make.rules
++++ b/kmer/Make.rules
+@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:%
+ ## EXE targets
+ ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
+ ${ALL_C_EXES}:
+- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
++ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
+ __SUBGOALS__+=$${${1:.=.C_EXES}}
+
+ ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
+ ${ALL_CXX_EXES}:
+- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
++ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
+ __SUBGOALS__+=$${${1:.=.CXX_EXES}}
+
+ define .RULE-install-copy-C-CXX-EXES
+diff --git a/kmer/configure.sh b/kmer/configure.sh
+index 2f0d5ea..9daf89f 100755
+--- a/kmer/configure.sh
++++ b/kmer/configure.sh
+@@ -254,13 +254,13 @@ EOF
+ # -*- makefile -*-
+ # Linux, optimized
+ CC := $CC
+-SHLIB_FLAGS := -shared
+-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CLDFLAGS := -L/usr/local/lib
++SHLIB_FLAGS := -shared ${LDFLAGS}
++CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CLDFLAGS :=
+ CLIBS := -pthread -ldl
+ CXX := $CXX
+-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CXXLDFLAGS := -L/usr/local/lib
++CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CXXLDFLAGS :=
+ CXXLIBS := -pthread -ldl
+ ARFLAGS := ruvs
+ INSTALL/ := $target/
+@@ -272,13 +272,13 @@ EOF
+ # -*- makefile -*-
+ # Linux64, optimized
+ CC := $CC
+-SHLIB_FLAGS := -shared
+-CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CLDFLAGS := -L/usr/local/lib
++SHLIB_FLAGS := -shared ${LDFLAGS}
++CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CLDFLAGS :=
+ CLIBS := -pthread -ldl
+ CXX := $CXX
+-CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+-CXXLDFLAGS := -L/usr/local/lib
++CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
++CXXLDFLAGS :=
+ CXXLIBS := -pthread -ldl
+ ARFLAGS := ruvs
+ INSTALL/ := $target/
+diff --git a/src/c_make.as b/src/c_make.as
+index 0172807..4304589 100644
+--- a/src/c_make.as
++++ b/src/c_make.as
+@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen
+
+ ifeq ($(OSTYPE), Linux)
+ ifeq ($(MACHINETYPE), i686)
+- ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++ LINK_LIBS += -pthread -lm
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+ ARCH_LIB = /usr/X11R6/lib
+ endif
+ ifeq ($(MACHINETYPE), amd64)
+- ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
++ LINK_LIBS += -pthread -lm
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+ ARCH_LIB = /usr/lib64 /usr/X11R6/lib64
+ endif
+ ifeq ($(MACHINETYPE), ia64)
+- ARCH_LDFLAGS += -pthread -lm
+- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
++ LINK_LIBS += -pthread -lm
++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+ ARCH_LIB = /usr/X11R6/lib
+ endif
+
+ ifeq ($(BUILDDEBUG), 1)
+- ARCH_CFLAGS += -g
+- ARCH_LDFLAGS +=
++ ARCH_CFLAGS +=
++ LINK_LIBS +=
+ else
+- ARCH_CFLAGS += -O2
+- ARCH_LDFLAGS += -Wl,-O1
++ ARCH_CFLAGS +=
++ LINK_LIBS +=
+ endif
+ endif
+
+@@ -94,19 +94,19 @@ endif
+
+ ifeq ($(OSTYPE), FreeBSD)
+ ifeq ($(MACHINETYPE), i386)
+- ARCH_LDFLAGS += -pthread -lthr -lm
+- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
++ LINK_LIBS += -pthread -lthr -lm
++ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+ endif
+ ifeq ($(MACHINETYPE), amd64)
+- ARCH_LDFLAGS += -pthread -lthr -lm
+- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
++ LINK_LIBS += -pthread -lthr -lm
++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
++ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+ endif
+
+ ifeq ($(BUILDCOVERAGE), 1)
+ ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage
+- ARCH_LDFLAGS += -lgcov
++ LINK_LIBS += -lgcov
+ else
+ ifeq ($(BUILDDEBUG), 1)
+ ARCH_CFLAGS += -g
+@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin)
+
+ ifeq ($(MACHINETYPE), i386)
+ ifeq ($(BUILDDEBUG), 1)
+- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
+- ARCH_LDFLAGS += -m64 -lm
++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
++ LINK_LIBS += -m64 -lm
+ else
+ # Wow, -Wshorten-64-to-32 is tough
+- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
+ # ARCH_CFLAGS += -Wextra
+ # ARCH_CFLAGS += -pedantic (see above about pedantic)
+- ARCH_LDFLAGS += -m64 -lm
++ LINK_LIBS += -m64 -lm
+ endif
+ endif
+
+@@ -161,23 +161,23 @@ endif
+ ifeq ($(OSTYPE), SunOS)
+ ifeq ($(MACHINETYPE), i86pc)
+ ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+- ARCH_LDFLAGS += -lm
++ LINK_LIBS += -lm
+ endif
+
+ ifeq ($(MACHINETYPE), sparc32)
+ ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+- ARCH_LDFLAGS += -lm -lnsl -lsocket
++ LINK_LIBS += -lm -lnsl -lsocket
+ endif
+
+ ifeq ($(MACHINETYPE), sparc64)
+ ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
+- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket
++ LINK_LIBS += -lm -lnsl -lsocket
+ endif
+
+ ifeq ($(BUILDDEBUG), 1)
+- ARCH_CFLAGS += -g
++ ARCH_CFLAGS +=
+ else
+- ARCH_CFLAGS += -O
++ ARCH_CFLAGS +=
+ endif
+ endif
+
+@@ -186,14 +186,14 @@ endif
+
+ ifeq ($(BUILDPROFILE), 1)
+ ARCH_CFLAGS += -pg
+- ARCH_LDFLAGS += -pg
++ LINK_LIBS += -pg
+ endif
+
+ # One can argue that CXXFLAGS should be separate. For now, we only
+ # add to the flags.
+
+ CFLAGS += $(ARCH_CFLAGS)
+-CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS)
++CXXFLAGS += $(ARCH_CXXFLAGS)
+ LDFLAGS += $(ARCH_LDFLAGS)
+
+ INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
+@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB)
+ OBJ_SEARCH_PATH = $(LOCAL_OBJ)
+
+ ifeq ($(SITE_NAME), JCVI)
+- LDFLAGS += -lcurl
++ LINK_LIBS += -lcurl
+ endif
+
+ # The order of compilation here is very carefully chosen to be the
+diff --git a/src/c_make.gen b/src/c_make.gen
+index 7b5227c..c27b777 100644
+--- a/src/c_make.gen
++++ b/src/c_make.gen
+@@ -396,12 +396,12 @@ $(LIBRARIES):
+ $(C_PROGS):
+ @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
+ cd $(LOCAL_OBJ); \
+- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
++ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
+
+ $(CXX_PROGS):
+ @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
+ cd $(LOCAL_OBJ); \
+- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
++ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
+
+ $(SCRIPT_PROGS): %.sh:
+ @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
new file mode 100644
index 000000000000..8e4a74368071
--- /dev/null
+++ b/sci-biology/wgs-assembler/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <upstream>
+ <remote-id type="sourceforge">wgs-assembler</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
new file mode 100644
index 000000000000..1ad4d9cf9540
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="x11-libs/libXt
+ !x11-terms/terminator"
+RDEPEND="${DEPEND}
+ app-shells/tcsh
+ dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+ sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+ -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+ "${S}"/src/c_make.as || die
+ sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+ -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+ "${S}"/kmer/configure.sh || die
+ cd "${S}/kmer"
+ ./configure.sh || die
+}
+
+src_compile() {
+ # not really an install target
+ emake -C kmer -j1 install || die
+ emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+ OSTYPE=$(uname)
+ MACHTYPE=$(uname -m)
+ MACHTYPE=${MACHTYPE/x86_64/amd64}
+ MY_S="${OSTYPE}-${MACHTYPE}"
+ sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+ sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+ sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+ sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+ dobin kmer/${MY_S}/bin/* || die
+ insinto /usr/$(get_libdir)/${PN}
+ doins kmer/${MY_S}/lib/* || die
+ # Collisions
+ # dolib.a kmer/${MY_S}/lib/* || die
+ insinto /usr/include/${PN}
+ doins kmer/${MY_S}/include/*
+
+ insinto /usr/share/${PN}
+ doins -r ${MY_S}/bin/spec
+ insinto /usr/share/${PN}/lib
+ doins -r ${MY_S}/bin/TIGR || die
+ rm -rf ${MY_S}/bin/{TIGR,spec}
+ dobin ${MY_S}/bin/* || die
+ dolib.a ${MY_S}/lib/* || die
+ dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
new file mode 100644
index 000000000000..8a9114d9ecd5
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 x86"
+
+DEPEND="x11-libs/libXt
+ !x11-terms/terminator"
+RDEPEND="${DEPEND}
+ app-shells/tcsh
+ dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+ sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+ -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+ "${S}"/src/c_make.as || die
+ sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+ -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+ "${S}"/kmer/configure.sh || die
+ cd "${S}/kmer"
+ ./configure.sh || die
+}
+
+src_compile() {
+ # not really an install target
+ emake -C kmer -j1 install || die
+ emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+ OSTYPE=$(uname)
+ MACHTYPE=$(uname -m)
+ MACHTYPE=${MACHTYPE/x86_64/amd64}
+ MY_S="${OSTYPE}-${MACHTYPE}"
+ sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+ sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+ sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+ sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+ dobin kmer/${MY_S}/bin/* || die
+ insinto /usr/$(get_libdir)/${PN}
+ doins kmer/${MY_S}/lib/* || die
+ # Collisions
+ # dolib.a kmer/${MY_S}/lib/* || die
+ insinto /usr/include/${PN}
+ doins kmer/${MY_S}/include/*
+
+ insinto /usr/share/${PN}
+ doins -r ${MY_S}/bin/spec
+ insinto /usr/share/${PN}/lib
+ doins -r ${MY_S}/bin/TIGR || die
+ rm -rf ${MY_S}/bin/{TIGR,spec}
+ dobin ${MY_S}/bin/* || die
+ dolib.a ${MY_S}/lib/* || die
+ dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
new file mode 100644
index 000000000000..b3ac7c30813b
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit eutils python toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="static-libs"
+
+DEPEND="
+ x11-libs/libXt
+ !x11-terms/terminator"
+RDEPEND="${DEPEND}
+ app-shells/tcsh
+ dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+pkg_setup() {
+ python_set_active_version 2
+ python_pkg_setup
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-build.patch
+ tc-export CC CXX
+}
+
+src_configure() {
+ cd "${S}/kmer"
+ ./configure.sh || die
+}
+
+src_compile() {
+ # not really an install target
+ emake -C kmer -j1 install
+ emake -C src -j1 SITE_NAME=LOCAL
+}
+
+src_install() {
+ OSTYPE=$(uname)
+ MACHTYPE=$(uname -m)
+ MACHTYPE=${MACHTYPE/x86_64/amd64}
+ MY_S="${OSTYPE}-${MACHTYPE}"
+ sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+ sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+ sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+ sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+ dobin kmer/${MY_S}/bin/*
+ insinto /usr/$(get_libdir)/${PN}
+ use static-libs && doins kmer/${MY_S}/lib/*
+
+ insinto /usr/include/${PN}
+ doins kmer/${MY_S}/include/*
+
+ insinto /usr/share/${PN}/lib
+ doins -r ${MY_S}/bin/TIGR
+ rm -rf ${MY_S}/bin/TIGR || die
+ dobin ${MY_S}/bin/*
+ use static-libs && dolib.a ${MY_S}/lib/*
+ dodoc README
+}
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
new file mode 100644
index 000000000000..e25a27c40026
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
+HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="x11-libs/libXt
+ !x11-terms/terminator"
+RDEPEND="${DEPEND}
+ app-shells/tcsh
+ dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+src_configure() {
+ sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
+ -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
+ "${S}"/src/c_make.as || die
+ sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
+ -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
+ "${S}"/kmer/configure.sh || die
+ cd "${S}/kmer"
+ ./configure.sh || die
+}
+
+src_compile() {
+ # not really an install target
+ emake -C kmer -j1 install || die
+ emake -C src -j1 SITE_NAME=LOCAL || die
+}
+
+src_install() {
+ OSTYPE=$(uname)
+ MACHTYPE=$(uname -m)
+ MACHTYPE=${MACHTYPE/x86_64/amd64}
+ MY_S="${OSTYPE}-${MACHTYPE}"
+ sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+ sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+ sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+ sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+ dobin kmer/${MY_S}/bin/* || die
+ insinto /usr/$(get_libdir)/${PN}
+ doins kmer/${MY_S}/lib/* || die
+ # Collisions
+ # dolib.a kmer/${MY_S}/lib/* || die
+ insinto /usr/include/${PN}
+ doins kmer/${MY_S}/include/*
+
+ insinto /usr/share/${PN}
+ doins -r ${MY_S}/bin/spec
+ insinto /usr/share/${PN}/lib
+ doins -r ${MY_S}/bin/TIGR || die
+ rm -rf ${MY_S}/bin/{TIGR,spec}
+ dobin ${MY_S}/bin/* || die
+ dolib.a ${MY_S}/lib/* || die
+ dodoc README
+}
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
new file mode 100644
index 000000000000..fc9cf9f0083c
--- /dev/null
+++ b/sci-biology/wise/Manifest
@@ -0,0 +1 @@
+DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
new file mode 100644
index 000000000000..1ec433f19227
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
@@ -0,0 +1,301 @@
+diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
+--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300
++++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300
+@@ -213,7 +213,7 @@
+ }
+ }
+
+-/* Function: getline()
++/* Function: get_line()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -377,7 +377,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -438,7 +438,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) get_line(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -587,7 +587,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -636,7 +636,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -816,7 +816,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
new file mode 100644
index 000000000000..d3c17098105e
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
@@ -0,0 +1,407 @@
+diff --git a/src/base/makefile b/src/base/makefile
+index 4620f19..a84e2c7 100644
+--- a/src/base/makefile
++++ b/src/base/makefile
+@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \
+
+
+ #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
+-CFLAGS = -c -O2 -DUNIX -pthread
+-LFLAGS = -g -lm
++CFLAGS += -c -DUNIX -pthread
++LFLAGS = -lm
+ DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
+ AR_OPTIONS = ru
+
+diff --git a/src/corba/makefile b/src/corba/makefile
+index df3dd78..237a1ba 100644
+--- a/src/corba/makefile
++++ b/src/corba/makefile
+@@ -1,10 +1,10 @@
+
+
+-CC = cc
++CC += gcc
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
+-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
+ LFLAGS = -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+
+@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl
+ orbit-idl hspscan_corba.idl
+
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
+- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o
+- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ .c.o :
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile
+index ef3334a..3a0bc2a 100644
+--- a/src/dnaindex/assembly/makefile
++++ b/src/dnaindex/assembly/makefile
+@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
+
+
+ CC = cc
+-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
++CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
+
+
+ .c.o :
+diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile
+index 285e6a0..8c6a0dc 100644
+--- a/src/dnaindex/makefile
++++ b/src/dnaindex/makefile
+@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
+
+
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
+- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+ make_shotgun : make_shotgun.o shotgun.o
+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
+@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o
+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
+
+ CC = cc
+-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
+
+
+ .c.o :
+diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile
+index d1d77af..cad8900 100644
+--- a/src/dynlibsrc/makefile
++++ b/src/dynlibsrc/makefile
+@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \
+
+
+
+-CC = cc
++CC ?= gcc
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags`
++CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
+ #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
+ LFLAGS = -g -L../base/ -lm
+ AR_OPTIONS = ru
+@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a
+ $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
+- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
++ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
+
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
+diff --git a/src/external/mott/makefile b/src/external/mott/makefile
+index 8d7c1d4..940c438 100644
+--- a/src/external/mott/makefile
++++ b/src/external/mott/makefile
+@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o
+ wise2_mott_bridge.o : wise2_mott_bridge.c
+ $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
+
+-CC = cc
++CC ?= gcc
+
+-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c
+-LFLAGS = -g -L../base/ -lm
++CFLAGS += -DPTHREAD -c
++LFLAGS = -L../base/ -lm
+ AR_OPTIONS = ru
+
+
+diff --git a/src/makefile b/src/makefile
+index bdff4ff..0d7c871 100644
+--- a/src/makefile
++++ b/src/makefile
+@@ -26,12 +26,12 @@
+
+ # Change the cc line to gcc if you get compiler errors
+ # Most likely you have a non ANSI C compiler
+-CC ?= cc
++CC ?= gcc
+
+ # These are the CFLAGS to use. These days Wise2 is inherently
+ # pthreaded, and everything is compiled with threads. More
+ # info on running threads can be found in the documentation
+-CFLAGS = -c -pthread -O2 `glib-config --cflags`
++CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags`
+
+
+
+diff --git a/src/models/makefile b/src/models/makefile
+index f518d0c..a297eff 100644
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -50,6 +50,8 @@ NEWG = geneparser21.o \
+ proteinsw.o \
+ estquick3.o
+
++EXTRALIBS += `pkg-config glib-2.0 --libs`
++
+ all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a
+
+ libmodel.a : $(NEWG)
+@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c
+ $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
+
+ oldpostwise : oldpostwise.o $(NEWG)
+- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
++ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
+
+ testdna : testdna.o dnaalign.o seqaligndisplay.o
+ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
+ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ scanwisep.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
+
+ hsp2aln_sw.o : hsp2aln_sw.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ scanwisep_mysql.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
+@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.
+
+
+ scanwisep_wiseserver.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
++ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
+
+ scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread
++ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
+
+ scanwisep_compress.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
+@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.
+
+
+ scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ localcishit.o : localcishit.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise.o : promoterwise.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
+- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread
+@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o
+ $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ genewise : genewise.o $(NEWG)
+- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o
+- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+
+ fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+
+ editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o
+- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
++ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
+
+
+ efgw : genewise.o $(NEWG)
+- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
+
+
+ genewisedb : genewisedb.o $(NEWG)
+- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ estwisedb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ edb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
+
+ estwise : estwise.o $(NEWG)
+- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+
+ amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o
+- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o
+- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o
+- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
+- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o
+- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
+- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG)
+- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+
+ HMMER_LIBS = ../HMMer2/
+@@ -345,11 +347,11 @@ HMMER_DEFINE =
+ CC = cc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
+ #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+diff --git a/src/network/makefile b/src/network/makefile
+index 303c2da..e607310 100644
+--- a/src/network/makefile
++++ b/src/network/makefile
+@@ -3,8 +3,8 @@
+
+ CC = cc
+ INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex
+-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags`
+-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs`
++CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+diff --git a/src/snp/makefile b/src/snp/makefile
+index ccf750a..2b83c43 100644
+--- a/src/snp/makefile
++++ b/src/snp/makefile
+@@ -2,12 +2,12 @@
+ .SUFFIXES : .dy
+
+
+-CC = cc
++CC ?= gcc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+
+ test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o
+- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
++ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
+
+ INCFLAGS = -I../base/ -I../dynlibsrc/
+ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
new file mode 100644
index 000000000000..42af0c7e849b
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
@@ -0,0 +1,302 @@
+diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
+index 5889e7d..bc95629 100644
+--- a/src/HMMer2/sqio.c
++++ b/src/HMMer2/sqio.c
+@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
+ }
+ }
+
+-/* Function: getline()
++/* Function: get_line()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@ readline(FILE *f, char *s)
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V)
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V)
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V)
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V)
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V)
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V)
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V)
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) get_line(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V)
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V)
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V)
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V)
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V)
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V)
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V)
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
new file mode 100644
index 000000000000..827ce4cdfa7a
--- /dev/null
+++ b/sci-biology/wise/files/wise-api.tex.patch
@@ -0,0 +1,38 @@
+--- api.tex.old 2005-03-06 11:31:59.862760952 -0500
++++ api.tex 2005-03-06 11:42:31.375756384 -0500
+@@ -204,7 +204,7 @@
+ \item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
+ \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
+ \item Read in the comparison matrix using CompMat (\ref{object_CompMat})
+-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
+ \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
+ \end{itemize}
+
+@@ -213,7 +213,7 @@
+ \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
+ \item Make a protein database from the single protein object (\ref{object_ProteinDB})
+ \item Make a protein database from a single fasta file (\ref{object_ProteinDB})
+-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
+ \item Show the Hscore object using a show function (\ref{object_Hscore})
+ \item Retrieve individual protein objects from the database by taking out the
+ DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
+@@ -232,7 +232,7 @@
+ \item Read in a codon table (\ref{object_CodonTable})
+ \item Make a random DNA model (\ref{object_RandomModelDNA})
+ \item Make an algorithm type (\ref{module_gwrap})
+-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
+ \item Run the actual algorithm (\ref{module_gwrap})
+ \item show the alignment using genedisplay (\ref{module_gwrap})
+ \end{itemize}
+@@ -5055,7 +5055,7 @@
+ Member functions of RandomModel
+
+ \section{sequence\_codon}
+-\label{module_sequence\_codon}
++\label{module_sequence_codon}
+ This module only contains factory methods
+
+ \subsection{sequence\_codon factory methods}
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
new file mode 100644
index 000000000000..3f781c80833b
--- /dev/null
+++ b/sci-biology/wise/files/wise-env
@@ -0,0 +1 @@
+WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/wise/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild
new file mode 100644
index 000000000000..f68686842689
--- /dev/null
+++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs versionator
+
+DESCRIPTION="Intelligent algorithms for DNA searches"
+HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~alpha amd64 ia64 ~sparc x86"
+IUSE="doc static-libs"
+
+RDEPEND="~sci-biology/hmmer-2.3.2"
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ dev-lang/perl
+ virtual/latex-base"
+
+S="${WORKDIR}"/${PN}$(delete_version_separator 3)
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-glibc-2.10.patch \
+ "${FILESDIR}"/${P}-cflags.patch
+ cd "${S}"/docs || die
+ cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
+ cat wise2api.tex temp.tex apiend.tex > api.tex || die
+ epatch "${FILESDIR}"/${PN}-api.tex.patch
+}
+
+src_compile() {
+ emake \
+ -C src \
+ CC="$(tc-getCC)" \
+ all
+ if use doc; then
+ cd "${S}"/docs || die
+ for i in api appendix dynamite wise2 wise3arch; do
+ latex ${i} || die
+ latex ${i} || die
+ dvips ${i}.dvi -o || die
+ done
+ fi
+}
+
+src_test() {
+ cd "${S}"/src || die
+ WISECONFIGDIR="${S}/wisecfg" emake test
+}
+
+src_install() {
+ dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb
+ use static-libs && \
+ dolib.a \
+ "${S}"/src/base/libwisebase.a \
+ "${S}"/src/dynlibsrc/libdyna.a \
+ "${S}"/src/models/libmodel.a
+
+ insinto /usr/share/${PN}
+ doins -r "${S}"/wisecfg
+
+ if use doc; then
+ insinto /usr/share/doc/${PF}
+ doins "${S}"/docs/*.ps
+ fi
+ newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
+}
diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest
new file mode 100644
index 000000000000..d2e3a2dba99c
--- /dev/null
+++ b/sci-biology/yass/Manifest
@@ -0,0 +1 @@
+DIST yass-1.14.tar.gz 235530 SHA256 f23da1c16cf98317ad11c085feede9790401e888a95d486b550f0c081d4c9018
diff --git a/sci-biology/yass/files/1.14-as-needed.patch b/sci-biology/yass/files/1.14-as-needed.patch
new file mode 100644
index 000000000000..e57503801c7a
--- /dev/null
+++ b/sci-biology/yass/files/1.14-as-needed.patch
@@ -0,0 +1,207 @@
+diff --git a/configure.ac b/configure.ac
+index 68453ef..3ecfd21 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul])
+ dnl 1) threads options
+
+ dnl abc) : with-threads option
+-AC_ARG_WITH(
+- threads,
+- [ --with-threads compile with all threads],
+- [threads="yes"],
+- [threads="no"])
++AC_ARG_ENABLE(
++ [threads],
++ AS_HELP_STRING([--enable-threads], [compile with all threads]))
+
+-if test "$threads" = "yes"; then
++AS_IF([test "x$enable_threads" = "xyes"], [
+ AC_MSG_RESULT(detected cpu parameter: threads);
+
+ dnl pthread library here ? (UNIX system)
+@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then
+ AC_MSG_RESULT(yes)
+ AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+ CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK "
+- LDFLAGS="$LDFLAGS -lpthread"
++ LIBS="$LIBS -lpthread"
+ else
+ AC_MSG_RESULT(no : disabling \"--with-threads\" parameter)
+ fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-threads\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
+-
+-
+-dnl a) : with-thread-fr option
+-AC_ARG_WITH(
+- thread-fr,
+- [ --with-thread-fr compile with two separate threads for Forward and Reverse sequence],
+- [thread_forward_reverse="yes"],
+- [thread_forward_reverse="no"])
+-
+-if test "$thread_forward_reverse" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-fr);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-fr\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
+-
+-
+-dnl b) : with-thread-aa option
+-AC_ARG_WITH(
+- thread-aa,
+- [ --with-thread-aa compile with two separate threads for Assemble and Align steps],
+- [thread_assemble_align="yes"],
+- [thread_assemble_align="no"])
+-
+-if test "$thread_assemble_align" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-aa);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-aa\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-dnl c) : with-thread-qc option
+-AC_ARG_WITH(
+- thread-qc,
+- [ --with-thread-qc compile with threads for the query chunks],
+- [thread_query_chunk="yes"],
+- [thread_query_chunk="no"])
+-
+-if test "$thread_query_chunk" = "yes"; then
+- AC_MSG_RESULT(detected cpu parameter: thread-qc);
+-
+- dnl pthread library here ? (UNIX system)
+- AC_MSG_CHECKING(for pthread lib)
+- AC_CHECK_LIB(pthread, pthread_create,
+- [have_pthread="yes"],
+- [have_pthread="no"])
+- if test "$have_pthread" = "yes"; then
+- AC_MSG_RESULT(yes)
+- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
+- CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK "
+- LDFLAGS="$LDFLAGS -lpthread"
+- else
+- AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter)
+- fi
+-
+-else
+- if test -s /proc/cpuinfo; then
+- AC_MSG_CHECKING(for multi-processor)
+- dnl Multithread advice
+- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
+- AC_MSG_RESULT(yes)
+- AC_MSG_RESULT(- try \"configure --with-thread-qc\")
+- else
+- AC_MSG_RESULT(no)
+- fi;
+- fi;
+-fi
+-
+-
+-
++])
+
+ dnl 2) : low-memory option
+-AC_ARG_WITH(
+- low-memory,
+- [ --with-low-memory use less memory, but can miss some repeats],
+- [low_memory="yes"],
+- [low_memory="no"])
++AC_ARG_ENABLE(
++ [lowmemory],
++ AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats]))
+
+-if test "$low_memory" = "yes"; then
++AS_IF([test "x$enable_lowmemory" = "xyes"], [
+ AC_MSG_RESULT(detected memory parameter: low memory);
+ CFLAGS=" $CFLAGS -DLOW_MEMORY "
+-else
+- AC_MSG_RESULT(detected memory parameter : plain memory)
+-fi
+-
+-
+-CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer "
+-LDFLAGS="$LDFLAGS -lm"
++])
+
+ AC_SUBST(CFLAGS)
+ AC_SUBST(LDFLAGS)
++
+ AM_WITH_DMALLOC
+ AM_INIT_AUTOMAKE
+ AC_CONFIG_FILES([Makefile
+diff --git a/src/Makefile.am b/src/Makefile.am
+index e456f94..8d90ca9 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -6,3 +6,4 @@
+ bin_PROGRAMS = yass
+ yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \
+ align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h
++yass_LDADD = -lm
diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml
new file mode 100644
index 000000000000..e4a717e691b2
--- /dev/null
+++ b/sci-biology/yass/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="dmalloc">Enable debugging with the dmalloc library</flag>
+ <flag name="lowmem">Build for environments with low amounts of memory</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/yass/yass-1.14-r1.ebuild b/sci-biology/yass/yass-1.14-r1.ebuild
new file mode 100644
index 000000000000..6476a839c935
--- /dev/null
+++ b/sci-biology/yass/yass-1.14-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit autotools eutils
+
+DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds"
+HOMEPAGE="http://bioinfo.lifl.fr/yass/"
+SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="dmalloc lowmem threads"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dmalloc? ( dev-libs/dmalloc )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${PV}-as-needed.patch
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_enable threads) \
+ $(use_enable lowmem lowmemory) \
+ $(use_with dmalloc)
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die
+ dodoc AUTHORS README NEWS || die
+}
diff --git a/sci-biology/yass/yass-1.14.ebuild b/sci-biology/yass/yass-1.14.ebuild
new file mode 100644
index 000000000000..c0d6242a201d
--- /dev/null
+++ b/sci-biology/yass/yass-1.14.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds"
+HOMEPAGE="http://bioinfo.lifl.fr/yass/"
+SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS README NEWS
+}