Mercurial > repos > iuc > stacks2_gstacks
view test-data/gentest.sh @ 2:1d839ead7ad3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
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date | Wed, 15 Jul 2020 17:24:38 -0400 |
parents | d35cb34f2b85 |
children | 7370bb65bad4 |
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#!/usr/bin/env bash eval "$(conda shell.bash hook)" conda activate __stacks@2.52 mkdir stacks_outputs denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf rm stacks_outputs/catalog.calls mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/ mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/ mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/ mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/ mv stacks_outputs/tsv2bam.log tsv2bam/ mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/ mv stacks_outputs/gstacks.log* gstacks/ mv stacks_outputs/populations.* populations/ mv stacks_outputs/denovo_map.log denovo_map/ rmdir stacks_outputs