Version bump, drop old

Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64

4 files changed, 16 insertions, 56 deletions

diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog
index 4034d48873cf..29ce6b1a7b58 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 1.3 2012/01/29 22:10:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.4 2012/04/07 23:32:18 weaver Exp $
+
+*gatk-1.5 (07 Apr 2012)
+
+  07 Apr 2012; Andrey Kislyuk <weaver@gentoo.org> -gatk-1.2.ebuild,
+  -gatk-1.3.ebuild, +gatk-1.5.ebuild:
+  Version bump, drop old
 
 *gatk-1.4 (29 Jan 2012)
 
diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest
index e4ffeda7eba6..6b40a1382dce 100644
--- a/sci-biology/gatk/Manifest
+++ b/sci-biology/gatk/Manifest
@@ -1,19 +1,17 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 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
 DIST gatk-1.4.tar.gz 10477541 RMD160 842dd7a61496de53fda42424a51bf3071ba21ac3 SHA1 cea9e12d52a073353c0af92225b6b42699e7582d SHA256 1365b920d8c043a414b2f28b5f499e07b29b310abf7de7e32f89579d3b4e53bc
-EBUILD gatk-1.2.ebuild 1146 RMD160 358cd2389210f7731adb5398e38de32103ca3b5d SHA1 f0c4f4cdde65a0904cc21e3d857efccafcc9c37b SHA256 d285531ed68de6c0af862947f194282940a1df22abb1c1ae3dacfd49e9016d17
-EBUILD gatk-1.3.ebuild 1146 RMD160 9112b52b47b82022f5967289ce918282086f25e2 SHA1 63c859f6a480c60c7a7579ee452320b122834058 SHA256 6c190e00df6c17990908f594523194ff57e06a30e1382565031203f0c3f1deb0
+DIST gatk-1.5.tar.gz 10559965 RMD160 23fc39116798203e05f4612de24541ed9ff43d5b SHA1 89fc94d80b7eae5f86401a8c2c3aa79017d5d557 SHA256 376a4d63f272627a2de84abd3e6a3f7fee4a339b6643af59eac53838865d279e
 EBUILD gatk-1.4.ebuild 1146 RMD160 46be498b89056d13c4e912d4adc5b0bd390b123f SHA1 926cec3974fdef2a2540001b2159f07ee9166ef9 SHA256 2a6c8aa6b1b587a5632fb90fde05d2567ea77dbaba75c9abbd56b54af6b036fe
+EBUILD gatk-1.5.ebuild 1146 RMD160 c490dbfa1fe0c49c9127d18f62c2e4b39bf0a09a SHA1 7bf491077811d2927f7728e1ddb30734465256f0 SHA256 3e71f5b3008423f2d0f4f0d800122a172d789394a38aa74145db3203a9b510a6
 EBUILD gatk-9999.ebuild 1153 RMD160 9c0b558ab1899d2b39dba8ec83f7cff19f613a7f SHA1 b462e6f2df102871625dd40ce3ae23aa77d11385 SHA256 d551d981a41fccae7d8528a9d884ed889bf0a3f48797a08e07a8291c5153b111
-MISC ChangeLog 635 RMD160 1ce298cc05cb32efe0af9a6ed49d2d57cea1e0d3 SHA1 fc8fdb1230996c1f697df754538ec72cc17ec82d SHA256 6ebd59630410ad3725bf0f3198dc9c029016b396d65bb726acf41b032bfc3c9d
+MISC ChangeLog 792 RMD160 c4e311044d1b857ce8f1f40159fbf6a4969dbfc5 SHA1 d37d33d6028833813f041efc0b6030fac822203c SHA256 3a51f1e75d3839589be0f4a3281aeb3b2d340f9bc7f806e55cf455ac784fe96b
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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 Version: GnuPG v1.4.11 (GNU/Linux)
 
-iEYEARECAAYFAk8lw9IACgkQ8xSwyhbn2OZP9wCglJLAIqSsNF42OzGMRhVE8GHO
-ffIAoK0fEjw/Gfj7Zy7viYjDoglxPZPf
-=04Jf
+iEYEARECAAYFAk+AzocACgkQ8xSwyhbn2Oa9sACgnXdd9mLJuSwwfdM97mFkBu+a
+ry8An0dfK1lVcdu+xvz6xKCO+/y6MldW
+=t8fo
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/gatk/gatk-1.3.ebuild b/sci-biology/gatk/gatk-1.3.ebuild
deleted file mode 100644
index 43ae46e02d20..000000000000
--- a/sci-biology/gatk/gatk-1.3.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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
-}
diff --git a/sci-biology/gatk/gatk-1.2.ebuild b/sci-biology/gatk/gatk-1.5.ebuild
index c15c610ed329..e1ee4da5d921 100644
--- a/sci-biology/gatk/gatk-1.2.ebuild
+++ b/sci-biology/gatk/gatk-1.5.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-1.2.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
+# $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=885c33a
+MY_HASH=c981d24
 
 EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"