Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate build-and-run-job-scripts.sh @ 10:5286f3b1c9c2 draft default tip

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planemo upload commit 363ef0a73d874c67326a67f51a78328906951248-dirty
author mingchen0919
date Fri, 30 Nov 2018 22:15:50 -0500
parents 94762f1cb779
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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