commit: 8e2cf825955ffa033248c1092a341a7ad5dea2ec Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Apr 22 14:07:45 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Apr 22 14:07:45 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e2cf825
sci-biology/picard: preparing last java7-compatible version and one for java8 Package-Manager: portage-2.2.28 sci-biology/picard/metadata.xml | 15 +++++++ sci-biology/picard/picard-1.141.ebuild | 73 +++++++++++++++++++++++++++++++++ sci-biology/picard/picard-2.2.2.ebuild | 74 ++++++++++++++++++++++++++++++++++ 3 files changed, 162 insertions(+) diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml new file mode 100644 index 0000000..513e863 --- /dev/null +++ b/sci-biology/picard/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Johann Schmitz (ercpe)</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">picard</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild new file mode 100644 index 0000000..ab65edb --- /dev/null +++ b/sci-biology/picard/picard-1.141.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2016 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/BAM/CRAM/VCF files" +HOMEPAGE="http://picard.sourceforge.net + http://broadinstitute.github.io/picard"; +#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"; +SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" # 2.2.2 is MIT instead, not sure when it changed away from Apache +SLOT="0" +IUSE="" +KEYWORDS="" + +CDEPEND="dev-java/snappy:1.0 + dev-java/cofoja:0 + dev-java/commons-jexl:2 + dev-java/ant-core:0" + +DEPEND=">=virtual/jdk-1.7 + dev-java/ant-apache-bcel:0 + test? ( + dev-java/testng:0 + dev-lang/R + ) + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.7 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_TEST_TARGET="test" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" +EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" + +java_prepare() { + mkdir -p "${S}"/lib || die + + # TODO: update the patch + #epatch "${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/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild new file mode 100644 index 0000000..b9e6917 --- /dev/null +++ b/sci-biology/picard/picard-2.2.2.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2016 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/BAM/CRAM/VCF files" +HOMEPAGE="http://picard.sourceforge.net + http://broadinstitute.github.io/picard"; +#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"; +SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="" + +CDEPEND="dev-java/snappy:1.0 + dev-java/cofoja:0 + dev-java/commons-jexl:2 + dev-java/ant-core:0" + +DEPEND=">=virtual/jdk-1.8 + dev-java/ant-apache-bcel:0 + test? ( + dev-java/testng:0 + dev-lang/R + ) + ${CDEPEND}" +# >=jdk8u66 +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_TEST_TARGET="test" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" +EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" + +java_prepare() { + mkdir -p "${S}"/lib || die + + # TODO: update the old patch + #epatch "${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 +}
