[med-svn] r11850 - in trunk/packages/trimmomatic/trunk/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Fri Jul 20 09:55:24 UTC 2012
Author: moeller
Date: 2012-07-20 09:55:24 +0000 (Fri, 20 Jul 2012)
New Revision: 11850
Added:
trunk/packages/trimmomatic/trunk/debian/README.source
trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
trunk/packages/trimmomatic/trunk/debian/trimmomatic.links
Modified:
trunk/packages/trimmomatic/trunk/debian/changelog
trunk/packages/trimmomatic/trunk/debian/control
trunk/packages/trimmomatic/trunk/debian/patches/series
trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
trunk/packages/trimmomatic/trunk/debian/rules
Log:
Updated trimmomatic to 0.22. Prepared to issue the
ITP, but do not want to hijack from Andreas who started
the packaging.
Added: trunk/packages/trimmomatic/trunk/debian/README.source
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/README.source (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/README.source 2012-07-20 09:55:24 UTC (rev 11850)
@@ -0,0 +1,4 @@
+The following files and directories where removed from the source tree:
+trimmomatic-0.22/lib/jbzip2-0.9.jar
+trimmomatic-0.22/old
+
Modified: trunk/packages/trimmomatic/trunk/debian/changelog
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/changelog 2012-07-20 09:42:29 UTC (rev 11849)
+++ trunk/packages/trimmomatic/trunk/debian/changelog 2012-07-20 09:55:24 UTC (rev 11850)
@@ -1,5 +1,13 @@
-trimmomatic (0.17-1) unstable; urgency=low
+trimmomatic (0.22-1) UNRELEASED; urgency=low
- * Initial release (Closes: #?????)
+ * New upstream version, initial release ().
+ * Added dependency on libjblip2-java
+ * Added symbolic link from trimmomatic.jar to trimmomatic-0.22.jar
+ -- Steffen Moeller <moeller at debian.org> Fri, 20 Jul 2012 11:15:20 +0200
+
+trimmomatic (0.17-1) UNRELEASED; urgency=low
+
+ * Initial packaging.
+
-- Andreas Tille <tille at debian.org> Fri, 18 Nov 2011 19:12:40 +0100
Modified: trunk/packages/trimmomatic/trunk/debian/control
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/control 2012-07-20 09:42:29 UTC (rev 11849)
+++ trunk/packages/trimmomatic/trunk/debian/control 2012-07-20 09:55:24 UTC (rev 11850)
@@ -3,16 +3,16 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), openjdk-6-jdk | java6-sdk | java7-jdk, javahelper, ant
-Standards-Version: 3.9.2
+Uploaders: Andreas Tille <tille at debian.org>, Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8), openjdk-6-jdk | java6-sdk | java7-jdk, javahelper, ant, libjbzip2-java
+Standards-Version: 3.9.3
Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/trimmomatic/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/trimmomatic/trunk/
Package: trimmomatic
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, libjbzip2-java
Description: flexible read trimming tool for Illumina NGS data
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and
@@ -34,4 +34,3 @@
depending on the Illumina pipeline used), either uncompressed or
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
extension.
-
Added: trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch 2012-07-20 09:55:24 UTC (rev 11850)
@@ -0,0 +1,29 @@
+Index: trimmomatic-0.22/build.xml
+===================================================================
+--- trimmomatic-0.22.orig/build.xml 2012-05-03 10:10:02.000000000 +0200
++++ trimmomatic-0.22/build.xml 2012-07-20 11:33:05.054589127 +0200
+@@ -2,7 +2,7 @@
+ <property name="version" value="0.22"/>
+
+ <property name="src" location="src" />
+- <property name="lib" location="lib" />
++ <property name="lib" location="/usr/share/java" />
+
+ <property name="distsrc" location="distSrc" />
+
+@@ -23,7 +23,7 @@
+ <target name="import" depends="init">
+ <copy todir="${dist_lib}">
+ <fileset dir="${lib}">
+- <include name="*.jar"/>
++ <include name="jbzip2.jar"/>
+ </fileset>
+ </copy>
+ </target>
+@@ -78,4 +78,4 @@
+ <delete dir="${dist}" />
+ </target>
+
+-</project>
+\ No newline at end of file
++</project>
Modified: trunk/packages/trimmomatic/trunk/debian/patches/series
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/series 2012-07-20 09:42:29 UTC (rev 11849)
+++ trunk/packages/trimmomatic/trunk/debian/patches/series 2012-07-20 09:55:24 UTC (rev 11850)
@@ -1 +1,2 @@
usage.patch
+buildxmlJbzip2.patch
Modified: trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/usage.patch 2012-07-20 09:42:29 UTC (rev 11849)
+++ trunk/packages/trimmomatic/trunk/debian/patches/usage.patch 2012-07-20 09:55:24 UTC (rev 11850)
@@ -1,16 +1,16 @@
---- trimmomatic_0.17.orig/src/org/usadellab/trimmomatic/TrimmomaticPE.java
-+++ trimmomatic_0.17/src/org/usadellab/trimmomatic/TrimmomaticPE.java
-@@ -127,6 +127,13 @@
-
- File trimLog=null;
-
-+ if(args.length<7)
-+ {
-+ System.out.println("Usage: TrimmomaticPE [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U> <trimmer1>...");
-+ System.out.format(" Only %s arguments provided but 7 are needed.\n", args.length);
-+ System.exit(1);
-+ }
+Index: trimmomatic-0.22/src/org/usadellab/trimmomatic/TrimmomaticPE.java
+===================================================================
+--- trimmomatic-0.22.orig/src/org/usadellab/trimmomatic/TrimmomaticPE.java 2012-05-14 12:53:52.000000000 +0200
++++ trimmomatic-0.22/src/org/usadellab/trimmomatic/TrimmomaticPE.java 2012-07-20 11:27:09.911360304 +0200
+@@ -308,9 +308,11 @@
+ }
+ }
+
+
- while(args[argIndex].startsWith("-") && argIndex<args.length)
+ if(args.length-argIndex<7 || badOption)
{
- String arg=args[argIndex++];
+ System.out.println("Usage: TrimmomaticPE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U> <trimmer1>...");
++ System.out.format(" Bad option or too few arguments provided (%s of min 7).\n", args.length);
+ System.exit(1);
+ }
+
Modified: trunk/packages/trimmomatic/trunk/debian/rules
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/rules 2012-07-20 09:42:29 UTC (rev 11849)
+++ trunk/packages/trimmomatic/trunk/debian/rules 2012-07-20 09:55:24 UTC (rev 11850)
@@ -7,5 +7,11 @@
%:
dh $@ --with javahelper
+override_dh_auto_build:
+ if [ ! -d dist/unpack ]; then mkdir -p dist/unpack; fi
+ touch dist/unpack/LICENCE
+ touch dist/unpack/AUTHORS
+ ant
+
get-orig-source:
uscan --verbose --force-download --repack --rename
Added: trunk/packages/trimmomatic/trunk/debian/trimmomatic.links
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/trimmomatic.links (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/trimmomatic.links 2012-07-20 09:55:24 UTC (rev 11850)
@@ -0,0 +1 @@
+usr/share/java/trimmomatic-0.22.jar usr/share/java/trimmomatic.jar
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