annotate test-data/gentest.sh @ 7:a3e86cd9cac7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author iuc
date Mon, 23 May 2022 17:52:54 +0000
parents c9b77ced9a78
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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1 #!/usr/bin/env bash
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c9b77ced9a78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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2 #eval "$(conda shell.bash hook)"
c9b77ced9a78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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3 #conda activate __stacks@2.52
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 mkdir stacks_outputs
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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6 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired &&
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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7 gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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8 rm stacks_outputs/catalog.calls
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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10 mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12 mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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14 mv stacks_outputs/tsv2bam.log tsv2bam/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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15 mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 mv stacks_outputs/gstacks.log* gstacks/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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17 mv stacks_outputs/populations.* populations/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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18 mv stacks_outputs/denovo_map.log denovo_map/
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 rmdir stacks_outputs