Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements (wrt #491816)

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0x77C501ED

5 files changed, 228 insertions, 9 deletions

diff --git a/sci-biology/picard/ChangeLog b/sci-biology/picard/ChangeLog
index 88d05b159caf..893782303e61 100644
--- a/sci-biology/picard/ChangeLog
+++ b/sci-biology/picard/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/picard
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v 1.3 2013/03/11 16:46:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v 1.4 2013/11/24 15:21:14 ercpe Exp $
+
+*picard-1.103 (24 Nov 2013)
+
+  24 Nov 2013; Johann Schmitz <ercpe@gentoo.org> +files/1.103-gentoo.patch,
+  +picard-1.103.ebuild, metadata.xml:
+  Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted
+  tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements
+  (wrt #491816)
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -15,4 +23,3 @@
   04 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +picard-1.58.ebuild,
   +metadata.xml:
   New package, ebuild written by me
-
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
index 057d92e729e5..b6997d06ce9a 100644
--- a/sci-biology/picard/Manifest
+++ b/sci-biology/picard/Manifest
@@ -1,14 +1,21 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA256
 
+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 1623 SHA256 a8bbbd98e4957da487f73bd989a748dfc614a0c0a1ec7d615fec7a7028d25f53 SHA512 b0c2757e6cabbeba8b22ce006d7e81a23f50783b2d9ea57196bcb1e1416e183e18806f96812c0b4b05281a5984219094e08d0fef877138f7d4c0dbd3bc1cb16f WHIRLPOOL 346ba985fd9d91c84b27bba515a2f2839d7c3817f6c8cd2b6249ebc3965aaab03778907b99df4b5fa48fff9ebefd78887ed4531e3406adcfdeac3e99a9524ac0
 EBUILD picard-1.58.ebuild 1052 SHA256 5b97cee24c7b6edc70efa00d2e8180c1d8790e25daa3edccbd9f963adee21725 SHA512 17a3659c177d42cb214935dd4b36559a73526169e4661a010b58369e9996e6cfd7466d88cf5242e485d5ce4682046afddc821b880d32e0ebcb29aed84652e2ab WHIRLPOOL 37440784aa2ec6306f9e3d60ad50fe9136f2ae3827e78c89ac1cf04b837af006770315856853a24cf2e976b5f0eb53208c5518a815ed837d678212f0741ec54f
 EBUILD picard-1.63.ebuild 1052 SHA256 7b5e15effed2459cb93cf7e3fffdfd0083b2d6a2be28d828a4a48b06c6b227f7 SHA512 cdece35eabb6039a2c3d87dadbcad5d00e4b58842045a016907926e35bf2a9b7175a4225fe1f0e091a0e160fe9a6c4572b5a071810166c887e0a0b5304f3f944 WHIRLPOOL 2a362c2430f566b49958582dd07512e715fbe555b61e156ba10a0b1a49e12aff3c8906cc9ea527dbfd26a85247d18cc051de6be9a9ac355faf46c25d58b9d0cd
-MISC ChangeLog 615 SHA256 f61d2afd1252046103fbad89990aad266ae36b66f87d1418dc660575dcd70e28 SHA512 2ff1e3b9480b4da2fe058ca586686a1d0027c73dd7b36240d1064a44cb42899ec53c1a743c3dd416b2eee56348bbb794f0d053feb76f4c4078f6a054bed2bc6b WHIRLPOOL 4d61a649a4ca1c5c10aba485754ffb34c8ebd6ef44c19aef4c79de682ed54998feee795ec42d71ca36e3705814766fdabd6c1d2bd4b799beeb0b09af43f6ac63
-MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
+MISC ChangeLog 930 SHA256 0a77eea896f5aaabaa5de7a541b0eef5d03448078aa7ecc34777d37453c40076 SHA512 5991b3deb0c3e02f1622c7353d16d4f8e1336a58c8e90ed08632cc793c8c8945678c1b320996c5634dd1ed9b1f4df68b663b3520bdc5c3706a2cba6167a6f92d WHIRLPOOL d0c091dac93fe6028ca1d5f47f2cb5cbce0e10ca9cd0a7f4411d6b1dd429fcd43e24483a474610e50b6c187d7672a53ebb806b1970261efefd140f3d69e7b2ba
+MISC metadata.xml 266 SHA256 1cba703019f754a8511e7ba3230f29da4d93dc635d12291d3208792259a1d87d SHA512 b9a967d56a4a878b52a8d900ccc309850d92ae9a67843e47da31b3e6e0440e19eec57e51c4419ce41e47bb2e32114aa1ec8de3ca6d1b84352e55a024b4c273bc WHIRLPOOL 5d0acb5f87d3afb0649923547fa74c854d80cfb62a9327d65658e9994ace1cf5e4da5ec96abe8806382b875b6db54bfe40bdb7669b65956f45501e54f3a78225
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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
index f17a827e3101..265affea91d0 100644
--- a/sci-biology/picard/metadata.xml
+++ b/sci-biology/picard/metadata.xml
@@ -1,5 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci-biology</herd>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>ercpe@gentoo.org</email>
+		<name>Johann Schmitz (ercpe)</name>
+	</maintainer>
 </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..7415a3888923
--- /dev/null
+++ b/sci-biology/picard/picard-1.103.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/picard-1.103.ebuild,v 1.1 2013/11/24 15:21:14 ercpe Exp $
+
+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="http://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
+}
\ No newline at end of file