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comparison mv_untar_gatk.sh @ 11:057bce4b4f93 draft default tip

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author elixir-it
date Wed, 02 Oct 2019 04:39:04 -0400
parents e3662508ee26
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10:e3662508ee26 11:057bce4b4f93
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 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar 5 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
6 6
7 else 7 else
8 echo GATK is present 8 echo GATK is present
9 fi 9 fi