# HG changeset patch
# User Dave Bouvier <dave@bx.psu.edu>
# Date 1396621628 14400
# Node ID f202477a521b903df11ce1bbae204b0c56d9a316
# Parent  751f4d177d8e50fb47e29dd4f6673b8258943695
Fix JAVA_JAR_PATH.

diff -r 751f4d177d8e -r f202477a521b realigner_target_creator.xml
--- a/realigner_target_creator.xml	Tue Apr 01 09:12:09 2014 -0400
+++ b/realigner_target_creator.xml	Fri Apr 04 10:27:08 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