commit: 748a9abdd6948868e36aa058ab158d4c4506fdd2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Mar 5 20:09:21 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Mar 5 20:09:21 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=748a9abd
added build.xml exported by author from Eclipse IDE (it doesn't work under ant eclasses in my hands) Package-Manager: portage-2.2.15 sci-biology/fastqc/ChangeLog | 5 +++ sci-biology/fastqc/fastqc-0.11.2.ebuild | 12 +++++-- sci-biology/fastqc/files/build.xml | 59 +++++++++++++++++++++++++++++++++ 3 files changed, 73 insertions(+), 3 deletions(-) diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index 6b6cbf5..b828a60 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Mar 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +files/build.xml, + fastqc-0.11.2.ebuild: + added build.xml exported by author from Eclipse IDE (it doesn't work under ant + eclasses in my hands) + *fastqc-0.11.2 (24 Feb 2015) 24 Feb 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> diff --git a/sci-biology/fastqc/fastqc-0.11.2.ebuild b/sci-biology/fastqc/fastqc-0.11.2.ebuild index b608266..dadc288 100644 --- a/sci-biology/fastqc/fastqc-0.11.2.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit java-pkg-2 eutils +inherit java-pkg-2 eutils java-ant-2 DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"; @@ -16,11 +16,17 @@ KEYWORDS="" IUSE="" DEPEND="sci-biology/picard - >=virtual/jre-1.5" -RDEPEND="${DEPEND}" + >=virtual/jre-1.5:*" +RDEPEND="${DEPEND} + >=virtual/jdk-1.5:* + dev-java/ant-core" S="${WORKDIR}"/FastQC +src_prepare(){ + cp "${FILESDIR}"/build.xml . || die +} + src_install(){ dobin fastqc run_fastqc.bat dodoc README.txt RELEASE_NOTES.txt diff --git a/sci-biology/fastqc/files/build.xml b/sci-biology/fastqc/files/build.xml new file mode 100644 index 0000000..c4a6920 --- /dev/null +++ b/sci-biology/fastqc/files/build.xml @@ -0,0 +1,59 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!-- WARNING: Eclipse auto-generated file. + Any modifications will be overwritten. + To include a user specific buildfile here, simply create one in the same + directory with the processing instruction <?eclipse.ant.import?> + as the first entry and export the buildfile again. --> +<project basedir="." default="build" name="FastQC"> + <property environment="env"/> + <property name="debuglevel" value="source,lines,vars"/> + <property name="target" value="1.5"/> + <property name="source" value="1.5"/> + <path id="FastQC.classpath"> + <pathelement location="bin"/> + <pathelement location="jbzip2-0.9.jar"/> + <pathelement location="sam-1.103.jar"/> + <pathelement location="cisd-jhdf5.jar"/> + </path> + <target name="init"> + <mkdir dir="bin"/> + <copy includeemptydirs="false" todir="bin"> + <fileset dir="."> + <exclude name="**/*.launch"/> + <exclude name="**/*.java"/> + </fileset> + </copy> + </target> + <target name="clean"> + <delete dir="bin"/> + </target> + <target depends="clean" name="cleanall"/> + <target depends="build-subprojects,build-project" name="build"/> + <target name="build-subprojects"/> + <target depends="init" name="build-project"> + <echo message="${ant.project.name}: ${ant.file}"/> + <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}"> + <src path="."/> + <classpath refid="FastQC.classpath"/> + </javac> + </target> + <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/> + <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler"> + <copy todir="${ant.library.dir}"> + <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/> + </copy> + <unzip dest="${ant.library.dir}"> + <patternset includes="jdtCompilerAdapter.jar"/> + <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/> + </unzip> + </target> + <target description="compile project with Eclipse compiler" name="build-eclipse-compiler"> + <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/> + <antcall target="build"/> + </target> + <target name="FastQCApplication"> + <java classname="uk.ac.babraham.FastQC.FastQCApplication" failonerror="true" fork="yes"> + <classpath refid="FastQC.classpath"/> + </java> + </target> +</project>
