Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate build-and-run-job-scripts.sh @ 8:94762f1cb779 draft

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planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
author mingchen0919
date Mon, 30 Apr 2018 16:15:39 -0400
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1 # run SHELL_SCRIPT within tool outputs directory
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2 cd ${REPORT_FILES_PATH}
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4 # build job-script.sh
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5 cat >temp.sh <<EOF
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7 cp ${X_r} read_1.fq
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8 cp ${X_R} read_2.fq
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10 fastqc \\
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11 -q \\
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12 -c ${X_c} \\
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13 -l ${X_l} \\
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14 ${X_d}/read_1.fq > read_1.log.txt 2>&1
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16 fastqc \\
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17 -q \\
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18 -c ${X_c} \\
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19 -l ${X_l} \\
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20 ${X_d}/read_2.fq > read_2.log.txt 2>&1
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22 EOF
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24 grep -v None temp.sh > job-1-script.sh
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25 rm temp.sh
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27 # run SHELL_SCRIPT
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28 sh job-1-script.sh
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30 # unzip outputs
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31 unzip -q read_1_fastqc.zip
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32 unzip -q read_2_fastqc.zip