Mercurial > repos > iuc > data_manager_fetch_refseq

annotate tool-data/all_fasta.loc.sample @ 3:4314700c39d5 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit f633fe1d97bedff14dbbffcbcc028a3ce9d1d1f2"
author iuc
date Sun, 19 Apr 2020 18:43:18 +0000
parents 214e68e8852c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
5 #TAB characters):
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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6 #
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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8 #
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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9 #So, all_fasta.loc could look something like this:
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
10 #
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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14 #
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
diff changeset
17 #such as with hg19 above.
214e68e8852c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
iuc
parents:
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18 #