[med-svn] r14365 - trunk/packages/trimmomatic/trunk/debian/patches

[Andreas Tille]

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);
- 			}
-