Mercurial > repos > mingchen0919 > aurora_skewer_site
comparison build-and-run-job-scripts.sh @ 0:a42e58c71e5b draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 30 Dec 2018 12:55:49 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:a42e58c71e5b |
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| 1 # run job scripts within the tool outputs directory | |
| 2 cd ${REPORT_FILES_PATH} | |
| 3 | |
| 4 #========== build and run job 1 script ============ | |
| 5 cat >temp.sh <<EOF | |
| 6 skewer \\ | |
| 7 ${X_A} \\ | |
| 8 ${X_B} \\ | |
| 9 -x ${X_x} \\ | |
| 10 -y ${X_y} \\ | |
| 11 -m ${X_m} \\ | |
| 12 -r ${X_r} \\ | |
| 13 -d ${X_D} \\ | |
| 14 -q ${X_q} \\ | |
| 15 -Q ${X_Q} \\ | |
| 16 -l ${X_l} \\ | |
| 17 -j ${X_j} \\ | |
| 18 -M ${X_M} \\ | |
| 19 -b ${X_b} \\ | |
| 20 -c ${X_b} \\ | |
| 21 -n ${X_n} \\ | |
| 22 -u ${X_u} \\ | |
| 23 -f ${X_f} \\ | |
| 24 -z ${X_z} \\ | |
| 25 -qiime ${X_E} \\ | |
| 26 -quiet ${X_F} \\ | |
| 27 -i ${X_i} \\ | |
| 28 -o trim > skewer.log.txt 2>&1 | |
| 29 EOF | |
| 30 | |
| 31 # remove empty input lines | |
| 32 grep -v '\-M \\' temp.sh |\ | |
| 33 grep -v 'None' |\ | |
| 34 grep -v 'NO_ARGUMENT_NO' |\ | |
| 35 sed 's/NO_ARGUMENT_YES//g' > job-1-script.sh | |
| 36 | |
| 37 rm temp.sh | |
| 38 | |
| 39 # run job 1 script | |
| 40 sh job-1-script.sh | |
| 41 | |
| 42 # rename log file | |
| 43 if [ -e trim-trimmed.log ]; then | |
| 44 cp trim-trimmed.log trim-trimmed.txt | |
| 45 fi |