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++];
_______________________________________________
debian-med-commit mailing list
[email protected]
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
