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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/fasta
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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
Diffstat (limited to 'sci-biology/fasta')
-rw-r--r--sci-biology/fasta/Manifest2
-rw-r--r--sci-biology/fasta/fasta-35.4.10.ebuild58
-rw-r--r--sci-biology/fasta/fasta-36.3.5e.ebuild79
-rw-r--r--sci-biology/fasta/files/35.4.10-ldflags.patch26
-rw-r--r--sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch74
-rw-r--r--sci-biology/fasta/metadata.xml11
6 files changed, 250 insertions, 0 deletions
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
new file mode 100644
index 00000000000..734131ee7f7
--- /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 00000000000..3fb4fb923a9
--- /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 00000000000..a9466820c4e
--- /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 00000000000..c3b7a9b5690
--- /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 00000000000..a6eeabfdf46
--- /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 00000000000..b98c9919d24
--- /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>