Mercurial > repos > elixir-it > covacs_apply_recalibrator

comparison mv_untar_gatk.sh @ 2:f47e8d9b7f2e draft default tip

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Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:29:44 -0400
parents 48dc4c9bc497
children
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1:48dc4c9bc497 2:f47e8d9b7f2e
1 #!/bin/bash 1 #!/bin/bash
2 #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm 2 #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
3 #and untar the archive 3 #and untar the archive
4 if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then 4 if [ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ] ; then
5 echo start untar ;
5 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar 6 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
6 7 echo all done
7 else 8 else
8 echo GATK is present 9 echo GATK is present
9 fi 10 fi
10 11