Mercurial > repos > iuc > stacks2_gstacks
comparison test-data/gentest.sh @ 4:7370bb65bad4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 11:29:04 +0000 |
| parents | 1d839ead7ad3 |
| children |
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| 3:eb784fa07f80 | 4:7370bb65bad4 |
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| 1 #!/usr/bin/env bash | 1 #!/usr/bin/env bash |
| 2 eval "$(conda shell.bash hook)" | 2 #eval "$(conda shell.bash hook)" |
| 3 conda activate __stacks@2.52 | 3 #conda activate __stacks@2.52 |
| 4 | |
| 5 | |
| 6 | |
| 7 | 4 |
| 8 mkdir stacks_outputs | 5 mkdir stacks_outputs |
| 9 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && | 6 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && |
| 10 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf | 7 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf |
| 11 rm stacks_outputs/catalog.calls | 8 rm stacks_outputs/catalog.calls |