# HG changeset patch
# User stef
# Date 1412766334 14400
# Node ID cdd80484429d1e2e268560012a301dd47f8681f0
# Parent  f97a25d9b2dc4fc007baa223403a63894e1479be
Uploaded

diff -r f97a25d9b2dc -r cdd80484429d falco.xml
--- a/falco.xml	Wed Oct 08 06:54:57 2014 -0400
+++ b/falco.xml	Wed Oct 08 07:05:34 2014 -0400
@@ -28,7 +28,7 @@
   <!-- command block to call script with default R environment -->
   <command interpreter="bash">
     <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
-    falco.sh $falco_cfg;
+    falco.sh $falco_cfg \$JAVA_JAR_PATH;
   </command>
   <!--
   <command interpreter="bash">
@@ -77,7 +77,6 @@
       html_out=$html_output
       vcf_out=$vcf_output
       out_path=${html_output.files_path}
-      jar_path=${JAVA_JAR_PATH}
     </configfile>
   </configfiles>