reinit the tree, so we can have metadata

4 files changed, 95 insertions, 0 deletions

diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest
new file mode 100644
index 000000000000..0bfa7d0cfa84
--- /dev/null
+++ b/sci-biology/gatk/Manifest
@@ -0,0 +1,6 @@
+DIST gatk-2.4.tar.gz 9106774 SHA256 db0be90ef5182866a1f936742fba20b317ce582556e19acb69de2a8894f7383a SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace WHIRLPOOL 1fa7a73f317db82c313ea112ffaa6466c2b17384f1ad8d06c74a3f4764dfd822f036cc2dc99890c157fc2c32ce299a4a7d0c73cafc72dd7ad955d75053745b2c
+EBUILD gatk-2.4.ebuild 914 SHA256 2520ab79fd82f6f22b5a70ddecf0ca27d368dfae9e8af55e8781ea97d4230af5 SHA512 a1a6fc27407bbc13247e866ed2dbc34428009091bf85e73776b5a47a95f8daca976060ecf092c4a68fee8afc1068f10aebc743e879b837b8ce0cf8ee461f6b6d WHIRLPOOL 53b8219fa5d5845ef4a1ee46e54d0d2bd82377284dd58e3d879b83187f72a2cc97072284ce7c8ad42154aeba1e3367759f966b6a859351dd94e79504dc8c50d5
+EBUILD gatk-9999.ebuild 899 SHA256 3951b5deea9081f8417024f976e30268d469b3636feda97b30957485dff8fb1c SHA512 1bffd684f48d50a84d4c0c55f6ed8ac10bfe7ca93d35ec32d282922ad8f1bdcee5aee284c4202cb547b9a332c3aaf32b4ebf5f4488b83856a9ac11f67f8b36a2 WHIRLPOOL 22c0b9c3c4c2ebcefc6c8be57097be69a93408ddbcea34f4051c5a00367d83bc2b6d366eecf5e3b881ac4dc5da25cfff1ba54ae9c6d6befe7d02e7812f9879d1
+MISC ChangeLog 2986 SHA256 48aba811073c7fd29bc04e07796c430290baa81f5ed6a7ea090cb2ea552df3a3 SHA512 b767dac7a1ce7d97f4e698684f4ec427e2170a9f2296d67b4ef768173377e169536cee95377bac4d2bb8640e23da887044c1bd1f8da02890e955a6a400970755 WHIRLPOOL 6a43a43136ce1e1bced58b6fca10e17ec23a21f7fd6c7c37e20c893ca4610a266f69071a4c1588eff7660adba9006633b52e6c8b38250975c190463866f61c79
+MISC ChangeLog-2015 1270 SHA256 9aab10f16c8e6afe3e4ae601f67c8effd9f1aafa2686c27840afdd359ea91f44 SHA512 02f5130b2615c68a952a5374f0401535e0cb4a8d7aeb8b420a6077caae8b6423dc480f9b88aeabdcd21ffbb9ad6064ad2b4d498827f42fdc83368c4ac848e035 WHIRLPOOL 53b1dab0452dfb0bcc7550ac3e16080ac7d8e647b61b02dc36ae10571404eca4198379ae84b60a3dc528a14b722c52b0159d8ea2e0770d32167fc2e53fa3deed
+MISC metadata.xml 349 SHA256 4a02ed79b669b9458e55ad200851ea6b35f5af76b3a867df5fa3661e265eceb3 SHA512 1605fb041826c7197edcd3658343ed3ac50aea7dfa53262700b9f9e1a45ee81df501e55bf1e8417201f0f2709b6b6e29bb6e5036b7c187846b4dec5e89903f54 WHIRLPOOL 2ffd8a0b69eb6d47aae4b65e5f23f4b7149f518b3e268743f44ae2034fd526aa82530369a2503fcd29819d19a729dcaec7e6ac9ea3f8387593b37ef7feb4fafd
diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild
new file mode 100644
index 000000000000..1a885b922b87
--- /dev/null
+++ b/sci-biology/gatk/gatk-2.4.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+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/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND="
+	>=virtual/jdk-1.6
+	${COMMON_DEPS}"
+RDEPEND="
+	>=virtual/jre-1.6
+	${COMMON_DEPS}"
+
+src_prepare() {
+	sed -i '/property name="ivy.home"/ s|${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-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
new file mode 100644
index 000000000000..fee2670ad219
--- /dev/null
+++ b/sci-biology/gatk/gatk-9999.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+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=""
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+COMMON_DEPS=""
+DEPEND="
+	>=virtual/jdk-1.6
+	dev-vcs/git
+	${COMMON_DEPS}"
+RDEPEND="
+	>=virtual/jre-1.6
+	${COMMON_DEPS}"
+
+src_prepare() {
+	sed -i '/property name="ivy.home"/ s|${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/metadata.xml b/sci-biology/gatk/metadata.xml
new file mode 100644
index 000000000000..8c1bb65774cc
--- /dev/null
+++ b/sci-biology/gatk/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">broadgsa/gatk</remote-id>
+  </upstream>
+</pkgmetadata>