Mercurial > repos > nate > data_manager_bowtie2_index_builder

annotate tool-data/all_fasta.loc.sample @ 0:6220ea344019 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 5c5d8acf6955dc4f404998ac7929f13363ef2c41
author nate
date Tue, 29 Jul 2025 17:13:06 +0000
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6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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1 #This file lists the locations and dbkeys of all the fasta files
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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2 #under the "genome" directory (a directory that contains a directory
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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3 #for each build). The script extract_fasta.py will generate the file
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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4 #all_fasta.loc. This file has the format (white space characters are
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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5 #TAB characters):
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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6 #
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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8 #
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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9 #So, all_fasta.loc could look something like this:
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff changeset
10 #
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff changeset
14 #
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff changeset
17 #such as with hg19 above.
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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18 #