Mercurial > repos > iuc > stacks2_procrad
comparison test-data/gentest.sh @ 0:9993234400f1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 11:00:33 -0400 |
| parents | |
| children | bd5ff77e2036 |
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| -1:000000000000 | 0:9993234400f1 |
|---|---|
| 1 #!/usr/bin/env bash | |
| 2 | |
| 3 mkdir stacks_outputs | |
| 4 | |
| 5 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && | |
| 6 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf | |
| 7 rm stacks_outputs/catalog.calls | |
| 8 | |
| 9 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/ | |
| 10 mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/ | |
| 11 mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/ | |
| 12 mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/ | |
| 13 mv stacks_outputs/tsv2bam.log tsv2bam/ | |
| 14 mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/ | |
| 15 mv stacks_outputs/gstacks.log* gstacks/ | |
| 16 mv stacks_outputs/populations.* populations/ | |
| 17 mv stacks_outputs/denovo_map.log denovo_map/ | |
| 18 | |
| 19 rmdir stacks_outputs |