Mercurial > repos > iuc > stacks2_refmap

comparison test-data/gentest.sh @ 4:54541bef380c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:19:44 +0000
parents 6e43ea81f086
children
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3:3a6eacfb5ab6 4:54541bef380c
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
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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