From 5fc10c2c3ee32b85def311482f5534a88bf7c7c3 Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Sun, 30 Sep 2012 17:17:21 +0000 Subject: Version bump, remove old, add git dep (Portage version: 2.2.0_alpha134/cvs/Linux x86_64) --- sci-biology/gatk/ChangeLog | 8 ++++++- sci-biology/gatk/gatk-1.4.ebuild | 44 --------------------------------------- sci-biology/gatk/gatk-1.5.ebuild | 44 --------------------------------------- sci-biology/gatk/gatk-1.6.ebuild | 45 ++++++++++++++++++++++++++++++++++++++++ 4 files changed, 52 insertions(+), 89 deletions(-) delete mode 100644 sci-biology/gatk/gatk-1.4.ebuild delete mode 100644 sci-biology/gatk/gatk-1.5.ebuild create mode 100644 sci-biology/gatk/gatk-1.6.ebuild (limited to 'sci-biology') diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog index 29ce6b1a7b58..771019451c2c 100644 --- a/sci-biology/gatk/ChangeLog +++ b/sci-biology/gatk/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/gatk # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.4 2012/04/07 23:32:18 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.5 2012/09/30 17:17:21 weaver Exp $ + +*gatk-1.6 (30 Sep 2012) + + 30 Sep 2012; Andrey Kislyuk -gatk-1.4.ebuild, + -gatk-1.5.ebuild, +gatk-1.6.ebuild: + Version bump, remove old, add git dep *gatk-1.5 (07 Apr 2012) diff --git a/sci-biology/gatk/gatk-1.4.ebuild b/sci-biology/gatk/gatk-1.4.ebuild deleted file mode 100644 index 1599395c237a..000000000000 --- a/sci-biology/gatk/gatk-1.4.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.4.ebuild,v 1.1 2012/01/29 22:10:21 weaver Exp $ - -EAPI=4 - -MY_HASH=8439a51 - -EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" - -EANT_BUILD_TARGET="dist" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" - -#inherit java-pkg-2 java-ant-2 git -inherit java-pkg-2 java-ant-2 - -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/tarball/${PV} -> ${P}.tar.gz" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -COMMON_DEPS="" -DEPEND=">=virtual/jdk-1.6 - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.6 - ${COMMON_DEPS}" - -S="${WORKDIR}/broadgsa-gatk-${MY_HASH}" - -src_prepare() { - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die - java-pkg-2_src_prepare -} - -src_install() { - java-pkg_dojar dist/*.jar - java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar - java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar -} diff --git a/sci-biology/gatk/gatk-1.5.ebuild b/sci-biology/gatk/gatk-1.5.ebuild deleted file mode 100644 index e1ee4da5d921..000000000000 --- a/sci-biology/gatk/gatk-1.5.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.5.ebuild,v 1.1 2012/04/07 23:32:18 weaver Exp $ - -EAPI=4 - -MY_HASH=c981d24 - -EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" - -EANT_BUILD_TARGET="dist" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" - -#inherit java-pkg-2 java-ant-2 git -inherit java-pkg-2 java-ant-2 - -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/tarball/${PV} -> ${P}.tar.gz" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~amd64" - -COMMON_DEPS="" -DEPEND=">=virtual/jdk-1.6 - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.6 - ${COMMON_DEPS}" - -S="${WORKDIR}/broadgsa-gatk-${MY_HASH}" - -src_prepare() { - sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die - java-pkg-2_src_prepare -} - -src_install() { - java-pkg_dojar dist/*.jar - java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar - java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar -} diff --git a/sci-biology/gatk/gatk-1.6.ebuild b/sci-biology/gatk/gatk-1.6.ebuild new file mode 100644 index 000000000000..3c5c9f20952c --- /dev/null +++ b/sci-biology/gatk/gatk-1.6.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.6.ebuild,v 1.1 2012/09/30 17:17:21 weaver Exp $ + +EAPI=4 + +MY_HASH=93333f0 + +EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" + +EANT_BUILD_TARGET="dist" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 git +inherit java-pkg-2 java-ant-2 + +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/tarball/${PV} -> ${P}.tar.gz" + +LICENSE="as-is" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +COMMON_DEPS="" +DEPEND=">=virtual/jdk-1.6 + dev-vcs/git + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS}" + +S="${WORKDIR}/broadgsa-gatk-${MY_HASH}" + +src_prepare() { + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar dist/*.jar + java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar + java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar +} -- cgit v1.2.3-65-gdbad