# HG changeset patch
# User Dave Bouvier <dave@bx.psu.edu>
# Date 1396621686 14400
# Node ID 5b8eaae854da4772c918196c86947b3f6ad1f29c
# Parent  b83a853a3156a208a45ac9ed7219df1369aabcbb
Fix JAVA_JAR_PATH.

diff -r b83a853a3156 -r 5b8eaae854da realigner_target_creator.xml
--- a/realigner_target_creator.xml	Tue Apr 01 10:49:33 2014 -0400
+++ b/realigner_target_creator.xml	Fri Apr 04 10:28:06 2014 -0400
@@ -15,7 +15,7 @@
        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
    #end if
    -p 'java 
-    -jar "${JAVA_JAR_PATH}/GenomeAnalysisTK.jar"
+    -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
     -T "RealignerTargetCreator"
     -o "${output_interval}"
     -et "NO_ET" ##ET no phone home