reinit the tree, so we can have metadata

4 files changed, 221 insertions, 0 deletions

diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
new file mode 100644
index 000000000000..1f11f5f1d299
--- /dev/null
+++ b/sci-biology/picard/Manifest
@@ -0,0 +1,6 @@
+AUX 1.103-gentoo.patch 5667 SHA256 83eea393354c3802cd367f42762bcbb53ac026c2d12188ca946295347950dd23 SHA512 966b0cc9ffc5bbf4b23c003538e01533344df496c38797ab84fcd2b382e91e003cc797a0c6ff5a878406b1fc169c1b044bce447b68770c665cec327762f08f6d WHIRLPOOL 6771393d7a39cdae83866918ce187d556ed697f41d55032eea85295f08cc660542136a9f9eaa23f9cec014743aa0099303c1cee206a0318951c8fd36f39e29af
+DIST picard-1.103.tar.bz2 15037887 SHA256 777af2a0aadd97a2b909160774e6e0ad99cef6de7763096f10660ccbe2baca63 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca WHIRLPOOL de5a0341473174bfc7a1f1b8d1b3b6122b212a1d964dda534912347595a3da9fe2a86692959df7375896292e3f3657a9c27c2f1694fca60d48ff23192b93b098
+EBUILD picard-1.103.ebuild 1513 SHA256 cb13c4568db1f87427ab63210509bf2923256cdfbfab7a127d7b124f780fa6c0 SHA512 e731bbabeed2d16707ad900a8a271143542c3c851c4becd240d79158b2f806bf5a4faf22b7c466427c406392faefc51628be621ec5b2d429a47a716d003a66c1 WHIRLPOOL 3c1175bae6571d1d0695ad5fe2a265ff9034edc4c06eaecda5ae8986fdb83b409a5b02d0636093ce0850b9c4be2da101fc680a07707669d4b81c58013cb7deea
+MISC ChangeLog 3023 SHA256 93871a990cda8fe9e0be77197112a6c54ea4486323827310de73c45d143ba53d SHA512 fbaef8ada3de1410d342ab67696c2549f0857e3119c17b78bfebd2aa8ddc0ae4123e0cc1bdd2ef674fdbd36f7ee315b87167acd448a866a095372b36de09a6c5 WHIRLPOOL 1740f06e70516e2913156fba826e0b9f365aafe49e0f762d72ca4e1324a1bd610e64fbc94b55691e22581fff0cae3cb4a598069233bd7b81c3675829b68b9db5
+MISC ChangeLog-2015 1173 SHA256 14e93cee8c7bb9d7b6bcc68969e61f79158c4eb25a56afc0ac24f942c6930b0c SHA512 4f8018322128e732a2a3129a44b823791e52552e1e0d3b7b28a70aaf5e9158bc10e720d890d52618d312b21c1672fc6fd6a9dc823afbd433d8da5eb229624ab7 WHIRLPOOL 8f5d86e04162091935675249f12ccf929e8a863bec7725c5481dc1b1cd0fe9982879de98fee8aba1a9afafa671b8c501065a21acbfdddabc94d878e8b29e0510
+MISC metadata.xml 452 SHA256 970078b6008df7fe4039ac06797a81e24e146293bfbaebc6536498bb1ed70bdb SHA512 ed6d1d46bfddc918f869d55be92079c75fd720a19b681b444e6214c94753a917e3a1621b4e4f9dbdc1a8e737e118856fb60e2d7a5dbebd6dc57ffc0391bb6eaf WHIRLPOOL 718f4ed4e8eb810120973a7dbf3538edb59adccdbc2bef647d4273541d9a14d0d8a55c5b199dabe65218b5c26adaea36a1b23c651f4071afac7e883849d70613
diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch
new file mode 100644
index 000000000000..00e89b95056a
--- /dev/null
+++ b/sci-biology/picard/files/1.103-gentoo.patch
@@ -0,0 +1,131 @@
+diff --git a/build.xml b/build.xml
+index fca2271..11f4fbd 100755
+--- a/build.xml
++++ b/build.xml
+@@ -52,9 +52,6 @@
+     <property name="testng.verbosity" value="2"/>
+     <property name="test.debug.port" value="5005" />  <!-- override on the command line if desired -->
+ 
+-    <property environment="env"/>
+-    <property name="java6.home" value="${env.JAVA6_HOME}"/>
+-
+     <condition  property="isUnix">
+         <os family="unix"/>
+     </condition>
+@@ -78,9 +75,6 @@
+             <pathelement location="${classes}"/>
+         </path>
+ 
+-        <path id="java6.lib.ref">
+-            <fileset dir="${java6.home}/lib" includes="*.jar"/>
+-        </path>
+     </target>
+ 
+     <!-- CLEAN -->
+@@ -94,10 +88,6 @@
+     </target>
+ 
+     <!-- COMPILE -->
+-    <target name="compile" depends="compile-src, compile-tests"
+-            description="Compile files without cleaning">
+-    </target>
+-
+     <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/>
+ 
+     <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning">
+@@ -138,7 +128,7 @@
+     </target>
+ 
+     <!-- TEST -->
+-    <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests">
++    <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests">
+         <taskdef resource="testngtasks" classpathref="classpath"/>
+         <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}"
+                 failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}"
+@@ -151,6 +141,8 @@
+             <classfileset dir="${classes.test}">
+                 <include name="**/Test*.class"/>
+                 <include name="**/*Test.class"/>
++		<exclude name="**/ValidateSamFileTest.class" />
++		<exclude name="**/VCFWriterUnitTest.class" />
+             </classfileset>
+             <jvmarg value="-Xmx2G"/>
+         </testng>
+@@ -165,7 +157,7 @@
+     </target>
+ 
+     <target name="single-test"
+-            depends="compile, compile-tests"
++            depends="compile-tests"
+             description="Compile and run a single test.">
+         <taskdef resource="testngtasks" classpathref="classpath"/>
+         <fail unless="name" message="Please provide input test: -Dname=..." />
+@@ -200,13 +192,12 @@
+         </jar>
+     </target>
+ 
+-    <target name="picard-jar" depends="compile"
++    <target name="picard-jar" depends="compile-src"
+             description="Builds picard-${picard-version}.jar for inclusion in other projects">
+         <mkdir dir="${dist}"/>
+         <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
+             <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
+             <fileset dir="${src.scripts}" includes="**/*.R"/>
+-            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
+             <manifest>
+                 <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
+                 <attribute name="Implementation-Vendor" value="Broad Institute"/>
+@@ -214,7 +205,7 @@
+         </jar>
+     </target>
+ 
+-    <target name="tribble-jar" depends="compile"
++    <target name="tribble-jar" depends="compile-src"
+             description="Builds tribble-${tribble-version}.jar for inclusion in other projects">
+         <mkdir dir="${dist}"/>
+         <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no">
+@@ -225,7 +216,7 @@
+         </copy>
+     </target>
+ 
+-    <target name="variant-jar" depends="compile"
++    <target name="variant-jar" depends="compile-src"
+             description="Builds variant-${variant-version}.jar for inclusion in other projects">
+         <mkdir dir="${dist}"/>
+         <jar destfile="${dist}/variant-${variant-version}.jar" compress="no">
+@@ -262,7 +253,7 @@
+         </javadoc>
+     </target>
+ 
+-    <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar">
++    <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar">
+         <delete dir="${command_tmp}"/>
+ 
+         <mkdir dir="${command_tmp}"/>
+@@ -344,7 +335,7 @@
+     </target>
+ 
+     <!-- ALL -->
+-    <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
++    <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
+         <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
+             <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
+             <zipfileset dir="${lib}" includes="snappy*.jar"/>
+@@ -468,8 +459,6 @@
+                    target="${javac.target}">
+                 <classpath refid="@{compile.classpath}"/>
+                 <compilerarg line="@{compiler.args}" />
+-                <!-- ensure that Java 6 bootclasspath is used -->
+-                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
+             </javac>
+         </sequential>
+     </macrodef>
+@@ -494,8 +483,6 @@
+                     <pathelement location="${classes}"/>
+                 </classpath>
+                 <compilerarg line="@{compiler.args}"/>
+-                <!-- ensure that Java 6 bootclasspath is used -->
+-                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
+             </javac>
+         </sequential>
+     </macrodef>
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
new file mode 100644
index 000000000000..513e8631c4c2
--- /dev/null
+++ b/sci-biology/picard/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>ercpe@gentoo.org</email>
+		<name>Johann Schmitz (ercpe)</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">picard</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild
new file mode 100644
index 000000000000..7a6111c87746
--- /dev/null
+++ b/sci-biology/picard/picard-1.103.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="5"
+
+JAVA_PKG_IUSE="doc source test"
+WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
+HOMEPAGE="http://picard.sourceforge.net/"
+SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/snappy:1.0
+	dev-java/cofoja:0
+	dev-java/commons-jexl:2
+	dev-java/ant-core:0"
+
+DEPEND=">=virtual/jdk-1.6
+	dev-java/ant-apache-bcel:0
+	test? (
+		dev-java/testng:0
+		dev-lang/R
+	)
+	${CDEPEND}"
+RDEPEND=">=virtual/jre-1.6
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_TEST_TARGET="test"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
+EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
+
+java_prepare() {
+	mkdir "${S}"/lib || die
+
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+
+	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *-${PV}.jar; do
+		java-pkg_newjar $i ${i/-${PV}/}
+		rm $i || die
+	done
+
+	java-pkg_dojar *.jar
+	for i in *.jar; do
+		java-pkg_dolauncher ${i/.jar/} --jar $i;
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}
+
+src_test() {
+	java-pkg-2_src_test
+}