Mercurial > repos > mingchen0919 > aurora_fastqc_site
comparison build-and-run-job-scripts.sh @ 2:c64267b9f754 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 30 Dec 2018 12:48:14 -0500 |
| parents | |
| children |
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| 1:92e3de11b9f8 | 2:c64267b9f754 |
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| 1 # run SHELL_SCRIPT within tool outputs directory | |
| 2 cd ${REPORT_FILES_PATH} | |
| 3 | |
| 4 # build job-script.sh | |
| 5 cat >temp.sh <<EOF | |
| 6 | |
| 7 cp ${X_r} read_1.fq | |
| 8 cp ${X_R} read_2.fq | |
| 9 | |
| 10 fastqc \\ | |
| 11 -q \\ | |
| 12 -c ${X_c} \\ | |
| 13 -l ${X_l} \\ | |
| 14 ${X_d}/read_1.fq > read_1.log.txt 2>&1 | |
| 15 | |
| 16 fastqc \\ | |
| 17 -q \\ | |
| 18 -c ${X_c} \\ | |
| 19 -l ${X_l} \\ | |
| 20 ${X_d}/read_2.fq > read_2.log.txt 2>&1 | |
| 21 | |
| 22 EOF | |
| 23 | |
| 24 grep -v None temp.sh > job-1-script.sh | |
| 25 rm temp.sh | |
| 26 | |
| 27 # run SHELL_SCRIPT | |
| 28 sh job-1-script.sh | |
| 29 | |
| 30 # unzip outputs | |
| 31 unzip -q read_1_fastqc.zip | |
| 32 unzip -q read_2_fastqc.zip |