Mercurial > repos > stef > falco

changeset 19:273a9b5d1a88 draft

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Uploaded
author stef
date Wed, 08 Oct 2014 07:38:03 -0400
parents abc82d7d6bf3
children 918d964f2949
files falco.sh
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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"