Mercurial > repos > mingchen0919 > aurora_dustmasker

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author mingchen0919
date Fri, 09 Nov 2018 15:25:01 -0500
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# run SHELL_SCRIPT within tool outputs directory
cd ${REPORT_FILES_PATH}


# generate dustmasker.sh script
cat >temp.sh <<EOF
dustmasker \\
  -in ${X_A} \\
  -window ${X_B} \\
  -level ${X_C} \\
  -linker ${X_D} \\
  -infmt ${X_E} \\
  -outfmt ${X_F} \\
  -parse_seqids ${X_G} \\
  -out masked_file.txt > dustmasker.log.txt 2>&1

EOF

grep -v 'NO_ARGUMENT_NO' temp.sh > dustmasker.sh
rm temp.sh

# run dustmasker job
sh dustmasker.sh