Version bump, remove old, add git dep

Package-Manager: portage-2.2.0_alpha134/cvs/Linux x86_64

4 files changed, 19 insertions, 58 deletions

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 <weaver@gentoo.org> -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/Manifest b/sci-biology/gatk/Manifest
index 6b40a1382dce..afc8d670ac83 100644
--- a/sci-biology/gatk/Manifest
+++ b/sci-biology/gatk/Manifest
@@ -1,17 +1,15 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
-DIST gatk-1.4.tar.gz 10477541 RMD160 842dd7a61496de53fda42424a51bf3071ba21ac3 SHA1 cea9e12d52a073353c0af92225b6b42699e7582d SHA256 1365b920d8c043a414b2f28b5f499e07b29b310abf7de7e32f89579d3b4e53bc
-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 792 RMD160 c4e311044d1b857ce8f1f40159fbf6a4969dbfc5 SHA1 d37d33d6028833813f041efc0b6030fac822203c SHA256 3a51f1e75d3839589be0f4a3281aeb3b2d340f9bc7f806e55cf455ac784fe96b
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+DIST gatk-1.6.tar.gz 10672645 SHA256 e056b54627bc4b2cf13a8de99c56852d96794fa7c48a80e678a2436dbc4c09df SHA512 bbcea8cb2644c80d5b2faa656c2d92621645bf53e91c6dd7267e85da27c01fd094b8834409bc1ff5bd15e37f689d9b317a37d6d02cc13d629b56eebdbfbd5786 WHIRLPOOL 29847ca8dba21a7c4f03551b09872a2cabb089f52adbe1c2427881f698c10fc09077559cfada23bda76cf3e9d21c3e12d07f19d5f1bfb884b8cd3ea88e7cf28f
+EBUILD gatk-1.6.ebuild 1159 SHA256 403010e3e39e8f50ae10136fc5cd7efe44283b938509339c4be8a7cb5c00390d SHA512 d219ab5e17188eefd5aaf0d68ec58090f58d8ed817fe8e0bc9b034563f294e37f9fd4fcd71d946a346fb264cbf40d71e0830dad2d95069bfc8abb8362c60409d WHIRLPOOL 73417fed2c258e927120cc047f41d564c89a4b25b5f028b6d5a640ebc27c9d2d17070b2ab86acbd8c44f3cc82f52634d24f4143efefa135dbfcfd1d6e1b37778
+EBUILD gatk-9999.ebuild 1153 SHA256 d551d981a41fccae7d8528a9d884ed889bf0a3f48797a08e07a8291c5153b111 SHA512 ce45e555d2fb32c3c2e7ec4509e90ab5d898fbfcfd38d8cc5fa95ad7df8c70365946e62dc7f0afbba0d6cf1226afc4e7164b8a56d6e153b90237d9437141e29c WHIRLPOOL 56ffafb6efdc77a10a77bc54d20ff5be46b01ec78cfe6d912e83707297f718ae0b7c08687bc1145a6ac0f89cb623880248009741abe6aa61669de63ae82ec504
+MISC ChangeLog 964 SHA256 5c108b06992eaa133cc7946a2873d1da1a2a0777c262a64a2ff6ccf5cb940390 SHA512 832cdcc237535a71ab3d2ac3cd85d81f7ce857fd7b90c63b739f19d34fb2d9f15666124130aacef3ce3a59ed585b0eea8901c38d8897200e081d5cbd256fda45 WHIRLPOOL a348b6b9f831598595809d120d989686b770d0cd1cf79034cdda4feecaa3d07e8adf11c6eec323913cd72273e0693f4bf1c3f18f3e96c637937570f8129e8e68
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
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 Version: GnuPG v1.4.11 (GNU/Linux)
 
-iEYEARECAAYFAk+AzocACgkQ8xSwyhbn2Oa9sACgnXdd9mLJuSwwfdM97mFkBu+a
-ry8An0dfK1lVcdu+xvz6xKCO+/y6MldW
-=t8fo
+iEYEAREIAAYFAlBofqcACgkQ8xSwyhbn2OZQgQCdHMdp7bjDQNPW15MEEuo/K5hU
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+=tGB4
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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-1.4.ebuild b/sci-biology/gatk/gatk-1.6.ebuild
index 1599395c237a..3c5c9f20952c 100644
--- a/sci-biology/gatk/gatk-1.4.ebuild
+++ b/sci-biology/gatk/gatk-1.6.ebuild
@@ -1,10 +1,10 @@
 # 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 $
+# $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=8439a51
+MY_HASH=93333f0
 
 EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
 
@@ -26,6 +26,7 @@ KEYWORDS="~amd64"
 
 COMMON_DEPS=""
 DEPEND=">=virtual/jdk-1.6
+	dev-vcs/git
 	${COMMON_DEPS}"
 RDEPEND=">=virtual/jre-1.6
 	${COMMON_DEPS}"