Mercurial > repos > elixir-it > covacs_apply_recalibrator

view mv_untar_gatk.sh @ 2:f47e8d9b7f2e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:29:44 -0400
parents 48dc4c9bc497
children
line wrap: on
line source

#!/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
        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