diff options
author | Johann Schmitz <ercpe@gentoo.org> | 2013-11-24 15:21:14 +0000 |
---|---|---|
committer | Johann Schmitz <ercpe@gentoo.org> | 2013-11-24 15:21:14 +0000 |
commit | 9409dc63740a5efb15f378c8e883affd521dfc03 (patch) | |
tree | 7ece7b49349fe16239fddf050ad23138d2d08a08 /sci-biology | |
parent | Version bump. (diff) | |
download | gentoo-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/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/picard/files/1.103-gentoo.patch | 131 | ||||
-rw-r--r-- | sci-biology/picard/metadata.xml | 6 | ||||
-rw-r--r-- | sci-biology/picard/picard-1.103.ebuild | 70 |
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 +}
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