Author: tille
Date: 2013-08-07 10:26:42 +0000 (Wed, 07 Aug 2013)
New Revision: 14365
Removed:
trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
Modified:
trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
trunk/packages/trimmomatic/trunk/debian/patches/series
Log:
Adapt patches to new upstream version
Modified: trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
2013-08-07 10:18:31 UTC (rev 14364)
+++ trunk/packages/trimmomatic/trunk/debian/patches/buildxmlJbzip2.patch
2013-08-07 10:26:42 UTC (rev 14365)
@@ -1,17 +1,15 @@
-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
+--- a/build.xml
++++ b/build.xml
@@ -2,7 +2,7 @@
- <property name="version" value="0.22"/>
+ <property name="version" value="0.30"/>
<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 @@
+ <property name="adapters" location="adapters" />
+
+@@ -25,7 +25,7 @@
<target name="import" depends="init">
<copy todir="${dist_lib}">
<fileset dir="${lib}">
@@ -20,10 +18,3 @@
</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 2013-08-07
10:18:31 UTC (rev 14364)
+++ trunk/packages/trimmomatic/trunk/debian/patches/series 2013-08-07
10:26:42 UTC (rev 14365)
@@ -1,2 +1 @@
-usage.patch
buildxmlJbzip2.patch
Deleted: trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/usage.patch 2013-08-07
10:18:31 UTC (rev 14364)
+++ trunk/packages/trimmomatic/trunk/debian/patches/usage.patch 2013-08-07
10:26:42 UTC (rev 14365)
@@ -1,16 +0,0 @@
-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 @@
- }
- }
-
-+
- if(args.length-argIndex<7 || badOption)
- {
- 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);
- }
-
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