# HG changeset patch
# User elixir-it
# Date 1570005068 14400
# Node ID 5058867ac48f532fef61f15d0fbd0e096964b190
# Parent  3a37867409fe6f680f50fd34584999ab2d5b0958
Uploaded

diff -r 3a37867409fe -r 5058867ac48f covacs_Select_Filtration.xml
--- a/covacs_Select_Filtration.xml	Thu Nov 15 15:57:12 2018 -0500
+++ b/covacs_Select_Filtration.xml	Wed Oct 02 04:31:08 2019 -0400
@@ -8,7 +8,7 @@
   <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
 
diff -r 3a37867409fe -r 5058867ac48f mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Thu Nov 15 15:57:12 2018 -0500
+++ b/mv_untar_gatk.sh	Wed Oct 02 04:31:08 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