Mercurial > repos > elixir-it > covacs_select_filtration

changeset 2:5058867ac48f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:31:08 -0400
parents 3a37867409fe
children
files covacs_Select_Filtration.xml mv_untar_gatk.sh
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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
 
--- 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