Mercurial > repos > stef > falco

changeset 24:4b4fba5eab4d draft

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Uploaded
author stef
date Wed, 08 Oct 2014 08:14:41 -0400
parents a19fec3d80c4
children 2210b89487c6
files falco.sh
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/falco.sh	Wed Oct 08 08:11:58 2014 -0400
+++ b/falco.sh	Wed Oct 08 08:14:41 2014 -0400
@@ -50,11 +50,11 @@
 
 ## executables
 #echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file
-echo "snpEff=$SNPEFF_JAR_PATH/" >> $init_file
+echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file
 #echo "snpSift=/ccagc/lib/SnpSift" >> $init_file
-echo "snpSift=$SNPEFF_JAR_PATH/" >> $init_file
+echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
 #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
-echo "varscan=$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
+echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
 
 ## files
 echo "targetBed=$BED_PATH" >> $init_file