# HG changeset patch
# User elixir-it
# Date 1570005544 14400
# Node ID 057bce4b4f934d8611bf6ce439ce2bc2d4aa18f3
# Parent  e3662508ee26852b4f3d2b97fedddf6a6532bcfb
Uploaded

diff -r e3662508ee26 -r 057bce4b4f93 mutect2.xml
--- a/mutect2.xml	Sun Sep 22 16:31:11 2019 -0400
+++ b/mutect2.xml	Wed Oct 02 04:39:04 2019 -0400
@@ -43,7 +43,7 @@
 
       ##TODO gatk mv_untar_gatk take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
       ##and move  .jar and  command is runned
-      sh $__tool_directory__/mv_untar_gatk.sh &&
+      bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
 
       java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -nct 4  -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
       #if $reference_source.reference_source_selector == "history"
diff -r e3662508ee26 -r 057bce4b4f93 mv_untar_gatk.sh
--- a/mv_untar_gatk.sh	Sun Sep 22 16:31:11 2019 -0400
+++ b/mv_untar_gatk.sh	Wed Oct 02 04:39:04 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