[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/

[Martin Mokrejs]

commit:     07d6f1753d0063d948bfc29120bec3d7894aa013
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul 27 16:21:21 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul 27 16:21:21 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=07d6f175

sci-biology/gatk: upstream uses maven instead of ant, adjust ebuilds

Package-Manager: portage-2.2.28

 sci-biology/gatk/gatk-3.6.ebuild  | 48 +++++++++++++++++++++++++++++++++++++
 sci-biology/gatk/gatk-9999.ebuild | 50 +++++++++++++++++++++++++++++++++++++++
 sci-biology/gatk/metadata.xml     | 11 +++++++++
 3 files changed, 109 insertions(+)

diff --git a/sci-biology/gatk/gatk-3.6.ebuild b/sci-biology/gatk/gatk-3.6.ebuild
new file mode 100644
index 0000000..d05d2f7
--- /dev/null
+++ b/sci-biology/gatk/gatk-3.6.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+	dev-java/maven-bin:*
+	dev-java/cofoja
+	${COMMON_DEPS}"
+RDEPEND="
+	>=virtual/jre-1.6
+	>=sci-biology/SnpEff-2.0.5
+	${COMMON_DEPS}"
+
+src_prepare() {
+	sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
+	java-pkg-2_src_prepare
+}
+
+src_install() {
+	mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+	find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \
+		java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned jar 'gatk-tools-public-3.6.jar'
+	done
+}
+
+pkg_postinst(){
+	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
+	einfo "installation layout gets more testing"
+}

diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
new file mode 100644
index 0000000..cdc6646
--- /dev/null
+++ b/sci-biology/gatk/gatk-9999.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+EANT_BUILD_TARGET="dist"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit git-2 java-pkg-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
+	dev-java/maven-bin:*
+	dev-java/cofoja
+	${COMMON_DEPS}"
+RDEPEND="
+	>=virtual/jre-1.6
+	>=sci-biology/SnpEff-2.0.5
+	${COMMON_DEPS}"
+
+src_prepare() {
+	sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
+	java-pkg-2_src_prepare
+}
+
+src_install() {
+	mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+	find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \
+		java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned jar 'gatk-tools-public-3.6.jar'
+	done
+}
+
+pkg_postinst(){
+	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
+	einfo "installation layout gets more testing"
+}

diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
new file mode 100644
index 0000000..8c1bb65
--- /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@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">broadgsa/gatk</remote-id>
+  </upstream>
+</pkgmetadata>