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annotate tool-data/all_fasta.loc.sample @ 4:fced964b054a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit ba82deebf385e4b2d4c55a43f34f0553478e6059
author iuc
date Fri, 09 Jun 2017 05:30:02 -0400
parents 26e3ae5f74ed
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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1 #This file lists the locations and dbkeys of all the fasta files
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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2 #under the "genome" directory (a directory that contains a directory
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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3 #for each build). The script extract_fasta.py will generate the file
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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4 #all_fasta.loc. This file has the format (white space characters are
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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5 #TAB characters):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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6 #
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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8 #
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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9 #So, all_fasta.loc could look something like this:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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10 #
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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14 #
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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15 #Your all_fasta.loc file should contain an entry for each individual
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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16 #fasta file. So there will be multiple fasta files for each build,
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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17 #such as with hg19 above.
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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18 #