Mercurial > repos > iuc > stacks2_refmap

comparison test-data/gentest.sh @ 2:6e43ea81f086 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 21:13:59 +0000
parents 524bd85b0bec
children 54541bef380c
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1:e1f99efbfd81 2:6e43ea81f086
1 #!/usr/bin/env bash 1 #!/usr/bin/env bash
2 eval "$(conda shell.bash hook)"
3 conda activate __stacks@2.52
4
5
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2 7
3 mkdir stacks_outputs 8 mkdir stacks_outputs
4
5 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && 9 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 10 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
7 rm stacks_outputs/catalog.calls 11 rm stacks_outputs/catalog.calls
8 12
9 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/ 13 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/