view test-data/gentest.sh @ 3:c207119ba5f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author iuc
date Tue, 27 Apr 2021 09:37:11 +0000
parents fcce77c09289
children 0345dbaaa79b
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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