# HG changeset patch
# User stef
# Date 1412766945 14400
# Node ID 6d8144665015290a3bbe4cb42d421997c7574344
# Parent  dc5e86a40851b344442b5947a80102fad86f916e
Uploaded

diff -r dc5e86a40851 -r 6d8144665015 falco.sh
--- a/falco.sh	Wed Oct 08 07:15:37 2014 -0400
+++ b/falco.sh	Wed Oct 08 07:15:45 2014 -0400
@@ -12,7 +12,8 @@
 #vcf_out=$4
 #out_path=$5
 source $1
-JAR_PATH=$2
+#JAR_PATH=$2
+#JAR_PATH=$3
 
 bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
 
@@ -41,7 +42,8 @@
 echo "MAN chosen:"$MAN_PATH
 #echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
 #echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
-echo "VARSCAN_PATH3:"$JAR_PATH
+echo "JAR_PATH1:"$jar_path2
+echo "JAR_PATH2:"$jar_path2
 
 init_file="galaxy_init.sh"
 echo '#!/bin/bash' > $init_file