Mercurial > repos > iuc > stacks2_procrad
comparison test-data/gentest.sh @ 4:9a171f9a450b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author | iuc |
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date | Wed, 01 Sep 2021 11:26:10 +0000 |
parents | bd5ff77e2036 |
children |
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3:e897c74a48bb | 4:9a171f9a450b |
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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 |