Mercurial > repos > elixir-it > covacs_apply_recalibrator

diff mv_untar_gatk.sh @ 2:f47e8d9b7f2e draft default tip

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Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:29:44 -0400
parents 48dc4c9bc497
children
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--- 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