# HG changeset patch
# User stef
# Date 1412767306 14400
# Node ID 5d9546a5bad52b0842f5e9cbcc8f4e2ba12e4427
# Parent  6d8144665015290a3bbe4cb42d421997c7574344
Uploaded

diff -r 6d8144665015 -r 5d9546a5bad5 falco.xml
--- a/falco.xml	Wed Oct 08 07:15:45 2014 -0400
+++ b/falco.xml	Wed Oct 08 07:21:46 2014 -0400
@@ -8,9 +8,12 @@
     <requirement type="package" version="2">varscan</requirement> 
     <requirement type="package" version="2">bcftools</requirement> 
     <!--
-    -->
+    
     <requirement type="set_environment">JAVA_JAR_PATH</requirement>
     <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
+    -->
+    <requirement type="set_environment">JAR_PATH1</requirement>
+    <requirement type="set_environment">JAR_PATH2</requirement>
     <requirement type="set_environment">TOOL_DIR</requirement>
   </requirements>
 
@@ -78,8 +81,10 @@
       html_out=$html_output
       vcf_out=$vcf_output
       out_path=${html_output.files_path}
-      jar_path1=\$JAVA_JAR_PATH
-      jar_path2=\$SNPEFF_JAR_PATH
+      jar_path1=\$JAR_PATH1
+      jar_path2=\$JAR_PATH2
+      jar_path3=\$JAVA_JAR_PATH
+      jar_path4=\$SNPEFF_JAR_PATH
     </configfile>
   </configfiles>