Mercurial > repos > stef > falco

changeset 13:6d8144665015 draft

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Uploaded
author stef
date Wed, 08 Oct 2014 07:15:45 -0400
parents dc5e86a40851
children 5d9546a5bad5
files falco.sh
diffstat 1 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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