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author elixir-it
date Wed, 02 Oct 2019 04:31:08 -0400
parents 3a37867409fe
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#!/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