Mercurial > repos > mingchen0919 > aurora_htseq_site
comparison build-and-run-job-scripts.sh @ 0:dcf65671e56a draft
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 30 Dec 2018 12:52:51 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:dcf65671e56a |
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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 >htseq-count.sh <<EOF | |
| 6 htseq-count \\ | |
| 7 $(echo ${X_A} | sed 's/,/ /g') \\ | |
| 8 ${X_G} \\ | |
| 9 -f ${X_f} \\ | |
| 10 -r ${X_r} \\ | |
| 11 -s ${X_S} \\ | |
| 12 -a ${X_a} \\ | |
| 13 -t ${X_T} \\ | |
| 14 -i ${X_i} \\ | |
| 15 -m ${X_m} > htseq-counts-raw.txt | |
| 16 | |
| 17 grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt | |
| 18 | |
| 19 EOF | |
| 20 | |
| 21 # run job 1 script | |
| 22 sh htseq-count.sh | |
| 23 |