Mercurial > repos > stef > falco

changeset 11:63f621915e89 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author stef
date Wed, 08 Oct 2014 07:05:41 -0400
parents cdd80484429d
children dc5e86a40851
files falco.sh
diffstat 1 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/falco.sh	Wed Oct 08 07:05:34 2014 -0400
+++ b/falco.sh	Wed Oct 08 07:05:41 2014 -0400
@@ -12,6 +12,7 @@
 #vcf_out=$4
 #out_path=$5
 source $1
+JAR_PATH=$2
 
 bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
 
@@ -38,9 +39,9 @@
 echo "MAN:"$manifest_file
 echo "BED chosen:"$BED_PATH
 echo "MAN chosen:"$MAN_PATH
-echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
-echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
-echo "VARSCAN_PATH3:"$jar_path
+#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH
+#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH
+echo "VARSCAN_PATH3:"$JAR_PATH
 
 init_file="galaxy_init.sh"
 echo '#!/bin/bash' > $init_file