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
-}
