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Wed, 27 Jul 2016 16:22:09 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 489087D4 for ; Wed, 27 Jul 2016 16:22:06 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1469636481.07d6f1753d0063d948bfc29120bec3d7894aa013.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gatk/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gatk/gatk-3.6.ebuild sci-biology/gatk/gatk-9999.ebuild sci-biology/gatk/metadata.xml X-VCS-Directories: sci-biology/gatk/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 07d6f1753d0063d948bfc29120bec3d7894aa013 X-VCS-Branch: master Date: Wed, 27 Jul 2016 16:22:06 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 756b0e5e-205d-4ee9-899b-aef0df15ae3a X-Archives-Hash: dc4117da684cac2d68d244a20e7ad4ed commit: 07d6f1753d0063d948bfc29120bec3d7894aa013 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jul 27 16:21:21 2016 +0000 Commit: Martin Mokrejs fold natur cuni 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 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + broadgsa/gatk + +