sci-biology/gatk: Version BUmp and move to MIT license

(Portage version: 2.2.0_alpha166/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

3 files changed, 28 insertions, 32 deletions

diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog
index 74753a2de7e5..c90933d00e07 100644
--- a/sci-biology/gatk/ChangeLog
+++ b/sci-biology/gatk/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/gatk
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.6 2013/03/11 15:11:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.7 2013/03/11 15:25:21 jlec Exp $
+
+*gatk-2.4 (11 Mar 2013)
+
+  11 Mar 2013; Justin Lecher <jlec@gentoo.org> -gatk-1.6.ebuild,
+  +gatk-2.4.ebuild, gatk-9999.ebuild:
+  Version BUmp and move to MIT license
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/gatk/gatk-1.6.ebuild b/sci-biology/gatk/gatk-2.4.ebuild
index 3c5c9f20952c..a472d8c12158 100644
--- a/sci-biology/gatk/gatk-1.6.ebuild
+++ b/sci-biology/gatk/gatk-2.4.ebuild
@@ -1,38 +1,32 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-2.4.ebuild,v 1.1 2013/03/11 15:25:21 jlec Exp $
 
-EAPI=4
-
-MY_HASH=93333f0
-
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
+EAPI=5
 
 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
+inherit java-pkg-2 java-ant-2 vcs-snapshot
 
 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} -> ${P}.tar.gz"
+SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="as-is"
+LICENSE="MIT"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64"
 
 COMMON_DEPS=""
-DEPEND=">=virtual/jdk-1.6
-	dev-vcs/git
+DEPEND="
+	>=virtual/jdk-1.6
 	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
+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
diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index b2e0ca49c1b1..29f7c51d4f5c 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.ebuild
@@ -1,38 +1,34 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.2 2013/03/11 15:25:21 jlec Exp $
 
-EAPI=4
-
-MY_HASH=885c33a
-
-EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
+EAPI=5
 
 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
+inherit git-2 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"
 SRC_URI=""
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
 
-LICENSE="as-is"
+LICENSE="MIT"
 SLOT="0"
 IUSE=""
 KEYWORDS=""
 
 COMMON_DEPS=""
-DEPEND=">=virtual/jdk-1.6
+DEPEND="
+	>=virtual/jdk-1.6
+	dev-vcs/git
 	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
+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