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-rw-r--r--sci-biology/ApE/ApE-2.0.7-r1.ebuild53
-rw-r--r--sci-biology/ApE/Manifest1
-rw-r--r--sci-biology/ApE/metadata.xml5
-rw-r--r--sci-biology/abyss/Manifest2
-rw-r--r--sci-biology/abyss/abyss-2.3.4.ebuild (renamed from sci-biology/abyss/abyss-2.0.3-r2.ebuild)31
-rw-r--r--sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch11
-rw-r--r--sci-biology/biopython/Manifest2
-rw-r--r--sci-biology/biopython/biopython-1.79.ebuild (renamed from sci-biology/biopython/biopython-1.77.ebuild)13
-rw-r--r--sci-biology/clustalw/clustalw-1.83-r4.ebuild4
-rw-r--r--sci-biology/gibbs/Manifest1
-rw-r--r--sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch11
-rw-r--r--sci-biology/gibbs/gibbs-3.1.ebuild47
-rw-r--r--sci-biology/gibbs/metadata.xml13
-rw-r--r--sci-biology/muscle/muscle-3.8.31.ebuild4
-rw-r--r--sci-biology/phyml/phyml-2.4.5-r3.ebuild4
-rw-r--r--sci-biology/picard/Manifest1
-rw-r--r--sci-biology/picard/files/1.103-gentoo.patch131
-rw-r--r--sci-biology/picard/metadata.xml11
-rw-r--r--sci-biology/picard/picard-1.103.ebuild69
-rw-r--r--sci-biology/stride/stride-20011129-r1.ebuild2
20 files changed, 28 insertions, 388 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild
deleted file mode 100644
index a56f5052520..00000000000
--- a/sci-biology/ApE/ApE-2.0.7-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-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 -> ${P}.zip"
-
-LICENSE="ApE"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-arch/unzip"
-RDEPEND="
- dev-lang/tcl:0
- dev-lang/tk:0"
-
-RESTRICT="bindist mirror"
-
-S="${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
deleted file mode 100644
index 6e45b2ff501..00000000000
--- a/sci-biology/ApE/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ApE-2.0.7.zip 318454 BLAKE2B 420001d298b8c6b1bc26247446aafe8c3adcf6477ebabc689219c094d46fe5e836d216a493169bac0ccd9c3b669d9421edb3b023a1a39cf74d32a81df09e66d2 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254
diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml
deleted file mode 100644
index 115e9d64a66..00000000000
--- a/sci-biology/ApE/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <!-- maintainer-needed -->
-</pkgmetadata>
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index e03409dd93f..9c9041e2c93 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1 +1 @@
-DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
+DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
index b9aed09d3ee..c2e1ffd29b3 100644
--- a/sci-biology/abyss/abyss-2.0.3-r2.ebuild
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -1,17 +1,17 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
inherit autotools toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-LICENSE="abyss"
+LICENSE="GPL-3"
SLOT="0"
-IUSE="+mpi openmp misc-haskell"
+IUSE="openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
RDEPEND="
@@ -21,24 +21,17 @@ RDEPEND="
dev-libs/gmp:0=
dev-libs/libffi:0=
)
- mpi? ( sys-cluster/openmpi )"
+ sys-cluster/openmpi
+ dev-db/sqlite:3
+"
DEPEND="${RDEPEND}
misc-haskell? (
dev-lang/ghc
- )"
-
-PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
-
-# GHC uses it's own native code generator. Portage's
-# QA check generates false positive because it assumes
-# presence of GCC-specific sections.
-#
-# Workaround false positiove by disabling the check completely.
-# bug #677600
-QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
+ )
+"
# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
+# todo: also allow build with mpich (--enable-mpich)
pkg_pretend() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
@@ -60,5 +53,5 @@ src_configure() {
# unless request by user: bug #534412
use misc-haskell || export ac_cv_prog_ac_ct_GHC=
- econf $(use_enable openmp)
+ econf $(use_enable openmp) --enable-maxk=256
}
diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
deleted file mode 100644
index d41c58ad261..00000000000
--- a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-https://bugs.gentoo.org/725300
---- a/configure.ac
-+++ b/configure.ac
-@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version])
- AC_CHECK_PROG(PANDOC, pandoc, yes)
- AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
-+AM_PROG_AR
-
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 420f6d1f83d..014c48aa840 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1 @@
-DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
+DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.79.ebuild
index 1dcbc2101c4..cef9a670130 100644
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ b/sci-biology/biopython/biopython-1.79.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 optfeature
@@ -33,9 +33,9 @@ python_test() {
cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
# need to create symlinks for doctests
- mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
- ln -r -s "${S}"/Bio/Align/substitution_matrices/data \
- "${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die
+ mkdir -p "${TEST_DIR}"/lib/Bio/Align || die
+ ln -r -s "${S}"/Bio/Align/substitution_matrices \
+ "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
cd "${TEST_DIR}"/lib/Tests || die
rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
@@ -54,8 +54,9 @@ python_install_all() {
pkg_postinst() {
optfeature_header "For database support you need to install:"
- optfeature "MySQL database support" dev-python/mysql-python
+ optfeature "MySQL database support" dev-python/mysqlclient
optfeature "PostgreSQL database support" dev-python/psycopg
+
optfeature_header "Some applications need extra packages:"
optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
}
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
index 144789f4c2a..076f16300b3 100644
--- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
LICENSE="clustalw"
SLOT="1"
-KEYWORDS="amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
IUSE=""
S="${WORKDIR}"/${PN}${PV}
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
deleted file mode 100644
index 24b52453c96..00000000000
--- a/sci-biology/gibbs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52
diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
deleted file mode 100644
index 6eaad637cfc..00000000000
--- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -51,7 +51,7 @@
- fi
- ])
-
--CFLAGS="$OPTFLAGS $MPIFLAGS -Wall -Werror $MACFLAG"
-+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"
-
- AC_PROG_CC([$COMP_LIST])
-
diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
deleted file mode 100644
index a06d0880ee4..00000000000
--- a/sci-biology/gibbs/gibbs-3.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
-HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
-SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="mpi"
-
-DEPEND="
- mpi? (
- virtual/mpi
- sys-cluster/mpe2
- )"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch )
-
-src_prepare() {
- default
- mv configure.{in,ac} || die
- eautoreconf
-}
-
-src_configure() {
- use mpi && export CC=mpicc
- econf $(use_enable mpi)
-}
-
-src_install() {
- default
-
- exeinto /usr/$(get_libdir)/${PN}
- doexe *.pl
-}
-
-pkg_postinst() {
- einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}."
- einfo "These scripts require installation of sci-biology/bioperl."
-}
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
deleted file mode 100644
index a0cd7b42b3a..00000000000
--- a/sci-biology/gibbs/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <longdescription>
- The Gibbs motif sampler stochastically examines candidate alignments
- in an effort to find the best alignment as measured by the maximum
- a posteriori (MAP) log-likelihood ratio.
- </longdescription>
-</pkgmetadata>
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
index 72c9a2c7e17..14781d000e7 100644
--- a/sci-biology/muscle/muscle-3.8.31.ebuild
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,7 +13,7 @@ SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
LICENSE="public-domain"
SLOT="0"
-KEYWORDS="amd64 ppc x86"
+KEYWORDS="amd64 ~ppc x86"
RDEPEND="!sci-libs/libmuscle"
diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
index 09877143063..ef969657357 100644
--- a/sci-biology/phyml/phyml-2.4.5-r3.ebuild
+++ b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="amd64 ppc x86"
+KEYWORDS="amd64 ~ppc x86"
IUSE=""
S=${WORKDIR}/${MY_P}
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
deleted file mode 100644
index 62dd6475dce..00000000000
--- a/sci-biology/picard/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST picard-1.103.tar.bz2 15037887 BLAKE2B a4df3aad9242749964a997698d80634e14ce19af575de9609655483eba247d0968cbdc856dbf00d854ec7eae37da8f3d047c50e4b78843e9d08441d9ef18eff6 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca
diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch
deleted file mode 100644
index 00e89b95056..00000000000
--- a/sci-biology/picard/files/1.103-gentoo.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-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:${toString:java6.lib.ref}"/>
- </javac>
- </sequential>
- </macrodef>
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
deleted file mode 100644
index 22fd62cbaa7..00000000000
--- a/sci-biology/picard/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">picard</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild
deleted file mode 100644
index 7a6111c8774..00000000000
--- a/sci-biology/picard/picard-1.103.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
-HOMEPAGE="http://picard.sourceforge.net/"
-SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${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 "${S}"/javadoc
-}
-
-src_test() {
- java-pkg-2_src_test
-}
diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
index 6211da2e92d..a8681b7f924 100644
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="
LICENSE="STRIDE"
SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
RESTRICT="mirror bindist"
S="${WORKDIR}"