# HG changeset patch
# User elixir-it
# Date 1570004984 14400
# Node ID f47e8d9b7f2e43c6c704ae1ee066f41916b11933
# Parent  48dc4c9bc4973fd60772638d5ac8051200d09399
Uploaded

diff -r 48dc4c9bc497 -r f47e8d9b7f2e covacs_ApplyRecalibrator.xml
--- a/covacs_ApplyRecalibrator.xml	Thu Nov 15 15:54:51 2018 -0500
+++ b/covacs_ApplyRecalibrator.xml	Wed Oct 02 04:29:44 2019 -0400
@@ -1,5 +1,5 @@
  <tool id="covacs_ApplyRecalibrator" name="covacs_ApplyRecalibrator" version="3.8">
-  <description>gatk ApplyRecalibrator wrapper </description>
+  <description>gatk ApplyRecalibrator wrapper for covacs</description>
   <macros>
 	<import>bed_macros.xml</import>
   </macros>
@@ -9,7 +9,7 @@
   <command>
     <![CDATA[
 	 ### call the .sh to untar the package 
-        sh $__tool_directory__/mv_untar_gatk.sh &&	
+	 bash $__tool_directory__/mv_untar_gatk.sh &> $log &&	
 
 
 	
diff -r 48dc4c9bc497 -r f47e8d9b7f2e mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Thu Nov 15 15:54:51 2018 -0500
+++ b/mv_untar_gatk.sh	Wed Oct 02 04:29:44 2019 -0400
@@ -1,9 +1,10 @@
 #!/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
+        echo start untar ; 
         tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
-
+	echo all done
 else
         echo GATK is present
 fi