commit: 07d6f1753d0063d948bfc29120bec3d7894aa013 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jul 27 16:21:21 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jul 27 16:21:21 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=07d6f175
sci-biology/gatk: upstream uses maven instead of ant, adjust ebuilds Package-Manager: portage-2.2.28 sci-biology/gatk/gatk-3.6.ebuild | 48 +++++++++++++++++++++++++++++++++++++ sci-biology/gatk/gatk-9999.ebuild | 50 +++++++++++++++++++++++++++++++++++++++ sci-biology/gatk/metadata.xml | 11 +++++++++ 3 files changed, 109 insertions(+) diff --git a/sci-biology/gatk/gatk-3.6.ebuild b/sci-biology/gatk/gatk-3.6.ebuild new file mode 100644 index 0000000..d05d2f7 --- /dev/null +++ b/sci-biology/gatk/gatk-3.6.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2016 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 + dev-java/maven-bin:* + dev-java/cofoja + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + >=sci-biology/SnpEff-2.0.5 + ${COMMON_DEPS}" + +src_prepare() { + sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff + java-pkg-2_src_prepare +} + +src_install() { + mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die + find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \ + java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned jar 'gatk-tools-public-3.6.jar' + done +} + +pkg_postinst(){ + einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the" + einfo "installation layout gets more testing" +} diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild new file mode 100644 index 0000000..cdc6646 --- /dev/null +++ b/sci-biology/gatk/gatk-9999.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2016 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 + +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 + dev-java/maven-bin:* + dev-java/cofoja + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + >=sci-biology/SnpEff-2.0.5 + ${COMMON_DEPS}" + +src_prepare() { + sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff + java-pkg-2_src_prepare +} + +src_install() { + mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die + find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \ + java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned jar 'gatk-tools-public-3.6.jar' + done +} + +pkg_postinst(){ + einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the" + einfo "installation layout gets more testing" +} diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml new file mode 100644 index 0000000..8c1bb65 --- /dev/null +++ b/sci-biology/gatk/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">broadgsa/gatk</remote-id> + </upstream> +</pkgmetadata>
