[gentoo-commits] proj/sci:master commit in: sci-biology/picard/files/, sci-biology/picard/

["Justin Lecher" <jlec@gentoo.org>]

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
-}