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annotate mv_untar_gatk.sh @ 10:e3662508ee26 draft

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author elixir-it
date Sun, 22 Sep 2019 16:31:11 -0400
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children 057bce4b4f93
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elixir-it
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1 #!/bin/bash
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elixir-it
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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
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elixir-it
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3 #and untar the archive
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elixir-it
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4 if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then
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elixir-it
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5 tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar
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elixir-it
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6
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elixir-it
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7 else
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elixir-it
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8 echo GATK is present
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elixir-it
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9 fi
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elixir-it
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