# HG changeset patch
# User yhoogstrate
# Date 1392719399 18000
# Node ID 7946b09020e02f20790fbf7498c8da3795421bda
# Parent  3f62f407068e6466058398a0e01ae7da2f0306b2
Uploaded

diff -r 3f62f407068e -r 7946b09020e0 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Tue Feb 18 05:29:50 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Tue Feb 18 05:29:59 2014 -0500
@@ -78,7 +78,7 @@
 			
 			 | java
 					 -Xmx64G
-					 -jar VarScan.v2.3.6.jar
+					 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
 						 mpileup2snp
 			 
 			#if $extended_parameters.parameters == "extended"