Mercurial > repos > iuc > data_manager_bwameth_index_builder

annotate tool-data/all_fasta.loc.sample @ 3:d1c0b1f0c67e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 8b77954efb8d46dfb3bec5421819076f3757ad06"
author iuc
date Sun, 26 Jan 2020 14:34:44 +0000
parents fa17303fc8de
children
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fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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2 #under the "genome" directory (a directory that contains a directory
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
5 #TAB characters):
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
6 #
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
8 #
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
10 #
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
14 #
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
17 #such as with hg19 above.
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
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18 #