# HG changeset patch
# User stef
# Date 1412768283 14400
# Node ID 273a9b5d1a88759afa30375f19a40b3afe6d172b
# Parent  abc82d7d6bf31147134e9f0507673b8961dfc9df
Uploaded

diff -r abc82d7d6bf3 -r 273a9b5d1a88 falco.sh
--- a/falco.sh	Wed Oct 08 07:37:56 2014 -0400
+++ b/falco.sh	Wed Oct 08 07:38:03 2014 -0400
@@ -12,7 +12,7 @@
 #vcf_out=$4
 #out_path=$5
 source $1
-#JAR_PATH=$2
+JAR_PATH=$2
 #JAR_PATH=$3
 
 bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
@@ -42,7 +42,7 @@
 echo "MAN chosen:"$MAN_PATH
 #echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
 #echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
-echo "JAR_PATH1:"$jar_path2
+echo "JAR_PATH1:"$JAR_PATH
 echo "JAR_PATH2:"$jar_path2
 
 init_file="galaxy_init.sh"