Mercurial > repos > elixir-it > covacs_variant_recalibrator

diff mv_untar_gatk.sh @ 5:c8dda6456827 draft

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author elixir-it
date Fri, 09 Nov 2018 08:53:14 -0500
parents 3d969c748317
children 14856ae90c1e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_gatk.sh	Fri Nov 09 08:53:14 2018 -0500
@@ -0,0 +1,9 @@
+#!/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
+	tar -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../ 
+	
+else
+	echo GATK is present
+fi