Mercurial > repos > matthias > stacks2_sstacks

annotate test-data/gentest.sh @ 7:0b0bc0e296f0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 11:00:55 -0400
parents 4068ef4253ab
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
1 #!/usr/bin/env bash
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
2
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
3 mkdir stacks_outputs
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
4
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
5 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired &&
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
6 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
7 rm stacks_outputs/catalog.calls
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
8
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
9 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
10 mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
11 mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
12 mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
13 mv stacks_outputs/tsv2bam.log tsv2bam/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
14 mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
15 mv stacks_outputs/gstacks.log* gstacks/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
16 mv stacks_outputs/populations.* populations/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
17 mv stacks_outputs/denovo_map.log denovo_map/
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
18
4068ef4253ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
19 rmdir stacks_outputs