Mercurial > repos > mingchen0919 > aurora_skewer

annotate build-and-run-job-scripts.sh @ 1:d74e8ffcf88f draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 13:56:16 -0500
parents 0358f6f78adf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0358f6f78adf planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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1 # run job scripts within the tool outputs directory
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2 cd ${REPORT_FILES_PATH}
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3
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4 #========== build and run job 1 script ============
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5 cat >temp.sh <<EOF
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6 skewer \\
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7 ${X_A} \\
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8 ${X_B} \\
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9 -x ${X_x} \\
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10 -y ${X_y} \\
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11 -m ${X_m} \\
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12 -r ${X_r} \\
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13 -d ${X_D} \\
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14 -q ${X_q} \\
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15 -Q ${X_Q} \\
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16 -l ${X_l} \\
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17 -j ${X_j} \\
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18 -M ${X_M} \\
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19 -b ${X_b} \\
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20 -c ${X_b} \\
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21 -n ${X_n} \\
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22 -u ${X_u} \\
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23 -f ${X_f} \\
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24 -z ${X_z} \\
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25 -qiime ${X_E} \\
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26 -quiet ${X_F} \\
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27 -i ${X_i} \\
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28 -o trim > skewer.log.txt 2>&1
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29 EOF
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30
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31 # remove empty input lines
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32 grep -v '\-M \\' temp.sh |\
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33 grep -v 'None' |\
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34 grep -v 'NO_ARGUMENT_NO' |\
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35 sed 's/NO_ARGUMENT_YES//g' > job-1-script.sh
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36
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37 rm temp.sh
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38
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39 # run job 1 script
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40 sh job-1-script.sh
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41
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42 # rename log file
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43 if [ -e trim-trimmed.log ]; then
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44 cp trim-trimmed.log trim-trimmed.txt
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45 fi