Mercurial > repos > mingchen0919 > aurora_dustmasker
comparison scripts_generator.sh @ 1:e0828838e0f3 draft default tip
update
| author | mingchen0919 |
|---|---|
| date | Fri, 09 Nov 2018 15:25:01 -0500 |
| parents | |
| children |
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| 0:b8c76b06d724 | 1:e0828838e0f3 |
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| 1 # run SHELL_SCRIPT within tool outputs directory | |
| 2 cd ${REPORT_FILES_PATH} | |
| 3 | |
| 4 | |
| 5 # generate dustmasker.sh script | |
| 6 cat >temp.sh <<EOF | |
| 7 dustmasker \\ | |
| 8 -in ${X_A} \\ | |
| 9 -window ${X_B} \\ | |
| 10 -level ${X_C} \\ | |
| 11 -linker ${X_D} \\ | |
| 12 -infmt ${X_E} \\ | |
| 13 -outfmt ${X_F} \\ | |
| 14 -parse_seqids ${X_G} \\ | |
| 15 -out masked_file.txt > dustmasker.log.txt 2>&1 | |
| 16 | |
| 17 EOF | |
| 18 | |
| 19 grep -v 'NO_ARGUMENT_NO' temp.sh > dustmasker.sh | |
| 20 rm temp.sh | |
| 21 | |
| 22 # run dustmasker job | |
| 23 sh dustmasker.sh |