# HG changeset patch
# User stef
# Date 1412770481 14400
# Node ID 4b4fba5eab4df8745983716568a55e326d763497
# Parent  a19fec3d80c4bc216ebe491e06534ad0a2f5cb28
Uploaded

diff -r a19fec3d80c4 -r 4b4fba5eab4d falco.sh
--- 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