[med-svn] r8612 - in trunk/packages/trimmomatic/trunk/debian: . bin patches

[Andreas Tille]

Author: tille
Date: 2011-11-19 10:52:47 +0000 (Sat, 19 Nov 2011)
New Revision: 8612

Added:
   trunk/packages/trimmomatic/trunk/debian/links
   trunk/packages/trimmomatic/trunk/debian/patches/
   trunk/packages/trimmomatic/trunk/debian/patches/series
   trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
Removed:
   trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE
Modified:
   trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE
   trunk/packages/trimmomatic/trunk/debian/install
Log:
Working wrapper script, patch to get some reasonable output when calling without any argument


Modified: trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE	2011-11-18 23:22:57 UTC (rev 8611)
+++ trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE	2011-11-19 10:52:47 UTC (rev 8612)
@@ -7,4 +7,5 @@
     echo "Broken installation of $PKGNAME.  JAR not found."
     exit 1
 fi
-java -classpath /usr/share/java/$JARVERSION org.usadellab.$PKGNAME.$FUNCNAME $@
+
+java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCNAME $@

Deleted: trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE	2011-11-18 23:22:57 UTC (rev 8611)
+++ trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE	2011-11-19 10:52:47 UTC (rev 8612)
@@ -1 +0,0 @@
-link TrimmomaticPE
\ No newline at end of file

Modified: trunk/packages/trimmomatic/trunk/debian/install
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/install	2011-11-18 23:22:57 UTC (rev 8611)
+++ trunk/packages/trimmomatic/trunk/debian/install	2011-11-19 10:52:47 UTC (rev 8612)
@@ -1,2 +1,2 @@
 dist/jar/*.jar	usr/share/java
-
+debian/bin/*	usr/bin

Added: trunk/packages/trimmomatic/trunk/debian/links
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/links	                        (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/links	2011-11-19 10:52:47 UTC (rev 8612)
@@ -0,0 +1 @@
+usr/bin/TrimmomaticPE	usr/bin/TrimmomaticSE

Added: trunk/packages/trimmomatic/trunk/debian/patches/series
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/patches/series	2011-11-19 10:52:47 UTC (rev 8612)
@@ -0,0 +1 @@
+usage.patch

Added: trunk/packages/trimmomatic/trunk/debian/patches/usage.patch
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/patches/usage.patch	                        (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/patches/usage.patch	2011-11-19 10:52:47 UTC (rev 8612)
@@ -0,0 +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);
++			}
++
+ 		while(args[argIndex].startsWith("-") && argIndex<args.length)
+ 			{
+ 			String arg=args[argIndex++];