# HG changeset patch
# User stef
# Date 1412766937 14400
# Node ID dc5e86a40851b344442b5947a80102fad86f916e
# Parent  63f621915e8920a5506ef59d95e72c4e0b33e364
Uploaded

diff -r 63f621915e89 -r dc5e86a40851 falco.xml
--- a/falco.xml	Wed Oct 08 07:05:41 2014 -0400
+++ b/falco.xml	Wed Oct 08 07:15:37 2014 -0400
@@ -28,7 +28,8 @@
   <!-- 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 \$JAVA_JAR_PATH;
+    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
+    falco.sh $falco_cfg;
   </command>
   <!--
   <command interpreter="bash">
@@ -77,6 +78,8 @@
       html_out=$html_output
       vcf_out=$vcf_output
       out_path=${html_output.files_path}
+      jar_path1=\$JAVA_JAR_PATH
+      jar_path2=\$SNPEFF_JAR_PATH
     </configfile>
   </configfiles>