Mercurial > repos > elixir-it > mutect2

diff mv_untar_gatk.sh @ 10:e3662508ee26 draft

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author elixir-it
date Sun, 22 Sep 2019 16:31:11 -0400
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children 057bce4b4f93
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_gatk.sh	Sun Sep 22 16:31:11 2019 -0400
@@ -0,0 +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
+        tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
+
+else
+        echo GATK is present
+fi
+