commit: 748a9abdd6948868e36aa058ab158d4c4506fdd2
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Mar 5 20:09:21 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Mar 5 20:09:21 2015 +
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 ${FILESDIR}/build.xml . || die
+}
+
src_install(){
dobin fastqc run_fastqc.bat
dodoc README.txt RELEASE_NOTES.txt
diff --git a/sci-biology/fastqc/files/build.xml
b/sci-biology/fastqc/files/build.xml
new file mode 100644
index 000..c4a6920
--- /dev/null
+++ b/sci-biology/fastqc/files/build.xml
@@ -0,0 +1,59 @@
+?xml version=1.0 encoding=UTF-8 standalone=no?
+!-- WARNING: Eclipse auto-generated file.
+ Any modifications will be overwritten.
+ To include a user specific buildfile here, simply create one in
the same
+ directory with the processing instruction ?eclipse.ant.import?
+ as the first entry and export the buildfile again. --
+project basedir=. default=build name=FastQC
+property environment=env/
+property name=debuglevel value=source,lines,vars/
+property name=target value=1.5/
+property name=source value=1.5/
+path id=FastQC.classpath
+pathelement location=bin/
+pathelement location=jbzip2-0.9.jar/
+pathelement location=sam-1.103.jar/
+pathelement location=cisd-jhdf5.jar/
+/path
+target name=init
+mkdir dir=bin/
+copy includeemptydirs=false todir=bin
+fileset dir=.
+exclude name=**/*.launch/
+exclude name=**/*.java/
+/fileset
+/copy
+/target
+target name=clean
+delete dir=bin/
+/target
+target depends=clean name=cleanall/
+target depends=build-subprojects,build-project name=build/
+target name=build-subprojects/
+target depends=init name=build-project
+echo message=${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
