diff options
| author |   Andrey Kislyuk <weaver@gentoo.org> | 2011-12-26 05:40:50 +0000 |
|---|---|---|
| committer | Andrey Kislyuk <weaver@gentoo.org> | 2011-12-26 05:40:50 +0000 |
| commit | 3a110cda33f8aa5484181fab7dee4f6818c63a5e (patch) | |
| tree | 30888e81bfef8f654c463b36fc215551c751fbe8 /sci-biology | |
| parent | Version bump (diff) | |
| download | historical-3a110cda33f8aa5484181fab7dee4f6818c63a5e.tar.gz historical-3a110cda33f8aa5484181fab7dee4f6818c63a5e.tar.bz2 historical-3a110cda33f8aa5484181fab7dee4f6818c63a5e.zip | |
Version bump
Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/gatk/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-biology/gatk/Manifest | 10 | ||||
| -rw-r--r-- | sci-biology/gatk/gatk-1.3.ebuild | 44 |
3 files changed, 56 insertions, 5 deletions
diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog index 2672b2663a32..9e2c8d21f8e6 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 1.1 2011/10/31 21:18:17 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.2 2011/12/26 05:40:50 weaver Exp $ + +*gatk-1.3 (26 Dec 2011) + + 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +gatk-1.3.ebuild: + Version bump *gatk-9999 (31 Oct 2011) *gatk-1.2 (31 Oct 2011) diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest index 92648ecea552..44adc391f3aa 100644 --- a/sci-biology/gatk/Manifest +++ b/sci-biology/gatk/Manifest @@ -2,14 +2,16 @@ Hash: SHA1 DIST gatk-1.2.tar.gz 6083390 RMD160 e514ea7f192af0688843e5851b9cde3b39cc557c SHA1 4a2f52efbc905dcf6de07c0e0d2771ce332cac42 SHA256 11be1a76fd8f06518bbd9de77096ebfd3d1aca555f40502c298f867c80b2958d +DIST gatk-1.3.tar.gz 10202135 RMD160 0d02258c06e8f3c1d2429f17ea27447b8e1ecd64 SHA1 98ec4d90702e7e7f1c045f64bff93cbdc50982b8 SHA256 2a4ad439df97951612ecb8ecbd1c650698372b7755634daf142ab5a296dc614c EBUILD gatk-1.2.ebuild 1146 RMD160 358cd2389210f7731adb5398e38de32103ca3b5d SHA1 f0c4f4cdde65a0904cc21e3d857efccafcc9c37b SHA256 d285531ed68de6c0af862947f194282940a1df22abb1c1ae3dacfd49e9016d17 +EBUILD gatk-1.3.ebuild 1146 RMD160 9112b52b47b82022f5967289ce918282086f25e2 SHA1 63c859f6a480c60c7a7579ee452320b122834058 SHA256 6c190e00df6c17990908f594523194ff57e06a30e1382565031203f0c3f1deb0 EBUILD gatk-9999.ebuild 1153 RMD160 9c0b558ab1899d2b39dba8ec83f7cff19f613a7f SHA1 b462e6f2df102871625dd40ce3ae23aa77d11385 SHA256 d551d981a41fccae7d8528a9d884ed889bf0a3f48797a08e07a8291c5153b111 -MISC ChangeLog 396 RMD160 aa92ab3f9ada175013a56ca62bc6d8b781e4e292 SHA1 65aded7eb23d97c3fa29df634943d3198c1c6219 SHA256 495435f4920fb78883d5d944ae49c2e71aba81820b861bc3ef851ce497afb8ed +MISC ChangeLog 505 RMD160 3eb7b78650e52fb117710b8d5e305c2594ec7025 SHA1 726b775f96465afa3e46e5f404198ed5b7b5a153 SHA256 3c54f72b555a2eb18036a9af9dcf78e65768ea5f2ee0051297e5a7e66b7d8d96 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) -iEYEARECAAYFAk6vEJ8ACgkQ8xSwyhbn2Oa0XwCdHYdJxLp7+tFoOrFNSZ1i1Fvm -VcsAn1Ize5jAzZn3KYmUPurHlvjg1tKq -=iocT +iEYEARECAAYFAk74COgACgkQ8xSwyhbn2OYqxwCgq607anGlvC8ssII/JaVcmWQi +ca8AmwSijLQR5cndF1DTp9GAImiCD3P0 +=cHKH -----END PGP SIGNATURE----- diff --git a/sci-biology/gatk/gatk-1.3.ebuild b/sci-biology/gatk/gatk-1.3.ebuild new file mode 100644 index 000000000000..43ae46e02d20 --- /dev/null +++ b/sci-biology/gatk/gatk-1.3.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.3.ebuild,v 1.1 2011/12/26 05:40:50 weaver Exp $ + +EAPI=4 + +MY_HASH=9dec377 + +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 +} |