Mercurial > repos > iuc > data_manager_bwameth_index_builder

annotate test-data/all_fasta.loc @ 6:fca923910aaa draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:46:50 +0000
parents 5ab25caa7b7d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
5 #TAB characters):
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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6 #
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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8 #
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
10 #
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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14 #
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
17 #such as with hg19 above.
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
diff changeset
18 #
5ab25caa7b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents:
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19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta