Mercurial > repos > mingchen0919 > aurora_skewer

annotate shell-script-template.sh @ 5:2c663ddb8488 draft

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author mingchen0919
date Wed, 25 Apr 2018 16:47:59 -0400
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children 5b07e567864b
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1 # SHELL_SCRIPT file name
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2 SHELL_SCRIPT='skewer.sh'
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3
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4 # run SHELL_SCRIPT within tool outputs directory
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5 cd ${REPORT_FILES_PATH}
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6
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7 # build job-script.sh
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8 cat >temp.sh <<EOF
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9 skewer \\
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10 ${X_A} \\
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11 ${X_B} \\
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12 -x ${X_x} \\
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13 -y ${X_y} \\
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14 -m ${X_m} \\
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15 -r ${X_r} \\
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16 -d ${X_D} \\
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17 -q ${X_q} \\
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18 -Q ${X_Q} \\
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19 -l ${X_l} \\
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20 -j ${X_j} \\
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21 -M ${X_M} \\
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22 -b ${X_b} \\
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23 -c ${X_b} \\
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24 -n ${X_n} \\
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25 -u ${X_u} \\
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26 -f ${X_f} \\
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27 -z ${X_z} \\
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28 -qiime ${X_E} \\
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29 -quiet ${X_F} \\
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30 -i ${X_i} \\
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31 -o trim > /dev/null 2>&1
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32 EOF
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33
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34 # remove empty input lines
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35 grep -v '\-M \\' temp.sh |\
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36 grep -v 'None' |\
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37 grep -v 'NO_ARGUMENT_NO' |\
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38 sed 's/NO_ARGUMENT_YES//g' > ${SHELL_SCRIPT}
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39
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40 rm temp.sh
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41
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42 # run SHELL_SCRIPT
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43 sh ${SHELL_SCRIPT}
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44
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45 # rename log file
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46 if [ -e trim-trimmed.log ]; then
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47 cp trim-trimmed.log trim-trimmed.txt
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48 fi