Mercurial > repos > elixir-it > covacs_haplotype_caller

changeset 3:b9b258d64d2b draft default tip

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Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:30:33 -0400
parents f34e1187b061
children
files covacs_HaplotypeCaller.xml mv_untar_gatk.sh
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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
--- 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