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

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.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 <mmokrejs@×××××××××××××××.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>