Mercurial > repos > devteam > data_manager_bowtie2_index_builder

annotate test-data/all_fasta.loc @ 13:8bf75f813413 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author iuc
date Thu, 05 Dec 2024 06:46:58 +0000
parents bb050998cee2
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bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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2 #under the "genome" directory (a directory that contains a directory
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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3 #for each build). The script extract_fasta.py will generate the file
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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5 #TAB characters):
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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6 #
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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8 #
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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9 #So, all_fasta.loc could look something like this:
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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10 #
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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14 #
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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17 #such as with hg19 above.
bb050998cee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
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18 #
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8bf75f813413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
parents: 6
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19 phiX174 phiX174 phiX 174 ${__HERE__}/phiX174.fasta