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| author |   Andrey Kislyuk <weaver@gentoo.org> | 2012-01-29 22:10:21 +0000 |
|---|---|---|
| committer | Andrey Kislyuk <weaver@gentoo.org> | 2012-01-29 22:10:21 +0000 |
| commit | d9edcf70089ae053aeb3b62d6f4f082086667613 (patch) | |
| tree | 46f680e2a4be75f712a5df825d986ba8064104bc /sci-biology | |
| parent | Call emake clean at the start of the compile phase to get rid of the prebuilt... (diff) | |
| download | gentoo-2-d9edcf70089ae053aeb3b62d6f4f082086667613.tar.gz gentoo-2-d9edcf70089ae053aeb3b62d6f4f082086667613.tar.bz2 gentoo-2-d9edcf70089ae053aeb3b62d6f4f082086667613.zip | |
Version bump, resolves bug 400885
(Portage version: 2.2.0_alpha74/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/gatk/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-biology/gatk/gatk-1.4.ebuild | 44 |
2 files changed, 51 insertions, 2 deletions
diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog index 9e2c8d21f8e6..4034d48873cf 100644 --- a/sci-biology/gatk/ChangeLog +++ b/sci-biology/gatk/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/gatk -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.2 2011/12/26 05:40:50 weaver Exp $ +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.3 2012/01/29 22:10:21 weaver Exp $ + +*gatk-1.4 (29 Jan 2012) + + 29 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +gatk-1.4.ebuild: + Version bump, resolves bug 400885 *gatk-1.3 (26 Dec 2011) diff --git a/sci-biology/gatk/gatk-1.4.ebuild b/sci-biology/gatk/gatk-1.4.ebuild new file mode 100644 index 000000000000..1599395c237a --- /dev/null +++ b/sci-biology/gatk/gatk-1.4.ebuild @@ -0,0 +1,44 @@ +# 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 +} |