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authorJohann Schmitz <ercpe@gentoo.org>2013-11-24 15:21:14 +0000
committerJohann Schmitz <ercpe@gentoo.org>2013-11-24 15:21:14 +0000
commit9409dc63740a5efb15f378c8e883affd521dfc03 (patch)
tree7ece7b49349fe16239fddf050ad23138d2d08a08 /sci-biology
parentVersion bump. (diff)
downloadgentoo-2-9409dc63740a5efb15f378c8e883affd521dfc03.tar.gz
gentoo-2-9409dc63740a5efb15f378c8e883affd521dfc03.tar.bz2
gentoo-2-9409dc63740a5efb15f378c8e883affd521dfc03.zip
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)
(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key 77C501ED)
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/picard/ChangeLog11
-rw-r--r--sci-biology/picard/files/1.103-gentoo.patch131
-rw-r--r--sci-biology/picard/metadata.xml6
-rw-r--r--sci-biology/picard/picard-1.103.ebuild70
4 files changed, 215 insertions, 3 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/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