Mercurial > repos > matthias > stacks2_cstacks

annotate test-data/gentest.sh @ 6:c8f5a29f720c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:57:24 -0400
parents 687f84474d33
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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1 #!/usr/bin/env bash
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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3 mkdir stacks_outputs
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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5 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired &&
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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6 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
687f84474d33 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
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
diff changeset
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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9 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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10 mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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11 mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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12 mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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13 mv stacks_outputs/tsv2bam.log tsv2bam/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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14 mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
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15 mv stacks_outputs/gstacks.log* gstacks/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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16 mv stacks_outputs/populations.* populations/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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17 mv stacks_outputs/denovo_map.log denovo_map/
687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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687f84474d33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
matthias
parents:
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19 rmdir stacks_outputs