commit: bec93ffba2d6dd56c7b10338771a91490bf1ce28 Author: Johann Schmitz <ercpe <AT> gentoo <DOT> org> AuthorDate: Sun Apr 24 06:15:26 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Apr 24 06:15:26 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bec93ffb
sci-biology/picard: brought ebuild for 2.2.2 to a somewhat workable state. Dropped test execution for now. Package-Manager: portage-2.2.26 sci-biology/picard/files/2.2.2-build.xml.patch | 115 +++++++++++++++++++++++++ sci-biology/picard/picard-2.2.2.ebuild | 48 +++-------- 2 files changed, 129 insertions(+), 34 deletions(-) diff --git a/sci-biology/picard/files/2.2.2-build.xml.patch b/sci-biology/picard/files/2.2.2-build.xml.patch new file mode 100644 index 0000000..278c4a1 --- /dev/null +++ b/sci-biology/picard/files/2.2.2-build.xml.patch @@ -0,0 +1,115 @@ +diff --git a/build.xml b/build.xml +index f0b98ab..14ff7f7 100755 +--- a/build.xml ++++ b/build.xml +@@ -83,15 +83,6 @@ + <!-- INIT --> + <target name="init"> + <path id="classpath"> +- <fileset dir="${htsjdk_lib_dir}"> +- <include name="*.jar"/> +- <include name="**/*.jar"/> +- </fileset> +- <!-- for the specific HTSJDK library JARs --> +- <fileset dir="${htsjdk}/lib"> +- <include name="*.jar"/> +- <include name="**/*.jar"/> +- </fileset> + <fileset dir="${lib}"> + <include name="**/*.jar"/> + </fileset> +@@ -117,53 +108,21 @@ + + <!-- HTS-JDK --> + <target name="set-htsjdk-version"> +- <!-- set the htsjdk version --> +- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/> +- <loadfile property="htsjdk-version" srcFile="${htsjdk}/htsjdk.version.properties"> +- <filterchain> +- <linecontains> +- <contains value="htsjdk-version="/> +- </linecontains> +- <tokenfilter> +- <replacestring from="htsjdk-version=" to=""/> +- </tokenfilter> +- <striplinebreaks/> +- </filterchain> +- </loadfile> + </target> + + <target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge"> +- <exec executable="git" failonerror="true"> +- <arg value="clone"/> +- <arg value="${htsjdk_git_url}"/> +- <arg value="${htsjdk}"/> +- </exec> + </target> + + <target name="compile-htsjdk" depends="set-htsjdk-version" description="Build HTS-JDK, and grab build jars"> +- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/> +- <ant antfile="build.xml" dir="${htsjdk}" target="all" inheritall="false"/> +- <copy todir="${htsjdk_lib_dir}"> +- <fileset dir="${htsjdk}/dist" includes="**/*-*.jar"/> +- <fileset dir="${htsjdk}/lib" includes="*.jar"/> +- </copy> +- <copy todir="${dist}"> +- <fileset dir="${htsjdk}/dist" includes="**/*.jar" excludes="**/*-*.jar"/> +- </copy> +- <!-- set the htsjdk version --> +- <ant antfile="build.xml" dir="${htsjdk}" target="write-version-property" inheritall="false"/> + </target> + + <target name="clean-htsjdk" description="Clean HTS-JDK"> +- <ant antfile="build.xml" dir="${htsjdk}" target="clean" inheritall="false"/> + </target> + + <target name="test-htsjdk" description="Test HTS-JDK"> +- <ant antfile="build.xml" dir="${htsjdk}" target="test" inheritall="false"/> + </target> + + <target name="compile-htsjdk-tests" description="Compile HTS-JDK Tests"> +- <ant antfile="build.xml" dir="${htsjdk}" target="compile-tests" inheritall="false"/> + </target> + + <!-- COMPILE --> +@@ -292,15 +251,11 @@ + <fileset dir="${lib}"> + <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing --> + </fileset> +- <fileset dir="${htsjdk_lib_dir}"> +- <include name="*.jar"/> +- </fileset> + </unjar> + + <jar destfile="${dist}/picard.jar" compress="no"> + <fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/> + <fileset dir="${src.scripts}" includes="**/*.R"/> +- <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/> + <fileset dir="${dist.tmp}" includes="**/*"/> + <fileset dir="${jar_opt}" includes="**/*"/> + +@@ -396,13 +351,9 @@ + <fileset dir="${lib}"> + <include name="**/*.jar"/> + </fileset> +- <fileset dir="${htsjdk}/dist"> +- <include name="**/*.jar"/> +- </fileset> + </classpath> + <fileset dir="."> + <include name="${src}/**/*.java"/> +- <include name="${htsjdk_src}/**/*.java"/> + </fileset> + <arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/> + </javadoc> +@@ -508,10 +459,8 @@ + description="Default build target"> + <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> + <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> +- <zipfileset dir="${htsjdk_lib_dir}" includes="htsjdk-*.jar" prefix="picard-tools-${picard-version}"/> + <zipfileset dir="${lib}" includes="snappy*.jar"/> + <!-- distribute libJniDeflater.so in same directory as jarfiles--> +- <zipfileset dir="${htsjdk}/lib/jni" includes="*" prefix="picard-tools-${picard-version}"/> + </zip> + </target> + diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild index b9e6917..c43b52c 100644 --- a/sci-biology/picard/picard-2.2.2.ebuild +++ b/sci-biology/picard/picard-2.2.2.ebuild @@ -2,73 +2,53 @@ # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI="5" +EAPI="6" -JAVA_PKG_IUSE="doc source test" -WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" +JAVA_PKG_IUSE="doc source" inherit java-pkg-2 java-ant-2 DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files" HOMEPAGE="http://picard.sourceforge.net http://broadinstitute.github.io/picard" -#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2" SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" IUSE="" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" -CDEPEND="dev-java/snappy:1.0 +CDEPEND="dev-java/snappy:1.1 dev-java/cofoja:0 dev-java/commons-jexl:2 - dev-java/ant-core:0" + dev-java/ant-core:0 + dev-java/htsjdk:0" DEPEND=">=virtual/jdk-1.8 - dev-java/ant-apache-bcel:0 - test? ( - dev-java/testng:0 - dev-lang/R - ) ${CDEPEND}" -# >=jdk8u66 + RDEPEND=">=virtual/jre-1.8 ${CDEPEND}" EANT_BUILD_TARGET="all" -EANT_TEST_TARGET="test" EANT_NEEDS_TOOLS="true" JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" -EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" +EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk" java_prepare() { - mkdir -p "${S}"/lib || die - - # TODO: update the old patch - #epatch "${FILESDIR}"/${PV}-gentoo.patch - - mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die + default + rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die + epatch "${FILESDIR}"/${PV}-build.xml.patch } src_install() { cd dist || die - for i in *-${PV}.jar; do - java-pkg_newjar $i ${i/-${PV}/} - rm $i || die - done + java-pkg_dojar ${PN}.jar + java-pkg_dojar ${PN}-lib.jar - java-pkg_dojar *.jar - for i in *.jar; do - java-pkg_dolauncher ${i/.jar/} --jar $i; - done + java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine use source && java-pkg_dosrc "${S}"/src/java/* use doc && java-pkg_dojavadoc "${S}"/javadoc } - -src_test() { - java-pkg-2_src_test -}