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view mv_untar_gatk.sh @ 1:48dc4c9bc497 draft

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author elixir-it
date Thu, 15 Nov 2018 15:54:51 -0500
parents c785cec34cdc
children f47e8d9b7f2e
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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