# HG changeset patch
# User elixir-it
# Date 1570005033 14400
# Node ID b9b258d64d2b76f379270a29aa08a3ba3f184ba7
# Parent  f34e1187b06141e42749d1f5ad4e2e70d6b2d77e
Uploaded

diff -r f34e1187b061 -r b9b258d64d2b covacs_HaplotypeCaller.xml
--- a/covacs_HaplotypeCaller.xml	Fri Nov 16 05:21:52 2018 -0500
+++ b/covacs_HaplotypeCaller.xml	Wed Oct 02 04:30:33 2019 -0400
@@ -10,7 +10,7 @@
   <command>
     <![CDATA[
 	### call the .sh to untar the package 
-        sh $__tool_directory__/mv_untar_gatk.sh &&
+	bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
 
 	##sym link to run GATK
 	#if $dbsnp
diff -r f34e1187b061 -r b9b258d64d2b mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Fri Nov 16 05:21:52 2018 -0500
+++ b/mv_untar_gatk.sh	Wed Oct 02 04:30:33 2019 -0400
@@ -1,7 +1,7 @@
 #!/bin/bash
 #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
 #and untar the archive
-if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then
+if [ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ] ; then
         tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
 
 else