# HG changeset patch
# User fcaramia
# Date 1357709738 18000
# Node ID 413ba6d9cc46ffcf88131729d278339cb55b7e22
# Parent  6a1b222df393b6f2773f044980230fe1d3e46b28
Uploaded

diff -r 6a1b222df393 -r 413ba6d9cc46 alignCustomAmplicon/alignCustomAmplicon_wrapper.xml
--- a/alignCustomAmplicon/alignCustomAmplicon_wrapper.xml	Wed Jan 09 00:27:53 2013 -0500
+++ b/alignCustomAmplicon/alignCustomAmplicon_wrapper.xml	Wed Jan 09 00:35:38 2013 -0500
@@ -8,6 +8,7 @@
   </requirements>
   <command interpreter="perl">
   	alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers 
+  	-j "\$JAVA_JAR_PATH/MergeSamFiles.jar"
   </command>
 
   <inputs>