Mercurial > repos > iuc > data_manager_hisat2_index_builder
annotate test-data/all_fasta.loc @ 7:d74c740bdb25 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
| author | iuc |
|---|---|
| date | Sun, 16 Apr 2023 08:30:13 +0000 |
| parents | 8eac26f44d29 |
| children |
| rev | line source |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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2 #under the "genome" directory (a directory that contains a directory |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
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3 #for each build). The script extract_fasta.py will generate the file |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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4 #all_fasta.loc. This file has the format (white space characters are |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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changeset
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5 #TAB characters): |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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6 # |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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8 # |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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9 #So, all_fasta.loc could look something like this: |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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10 # |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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changeset
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14 # |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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changeset
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15 #Your all_fasta.loc file should contain an entry for each individual |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
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16 #fasta file. So there will be multiple fasta files for each build, |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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changeset
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17 #such as with hg19 above. |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
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18 # |
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8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
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19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |