Mercurial > repos > devteam > data_manager_picard_index_builder

annotate test-data/all_fasta.loc @ 3:ae080ff506fd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
author iuc
date Mon, 03 Feb 2020 17:27:33 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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2 #under the "genome" directory (a directory that contains a directory
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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3 #for each build). The script extract_fasta.py will generate the file
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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5 #TAB characters):
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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6 #
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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8 #
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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9 #So, all_fasta.loc could look something like this:
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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10 #
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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14 #
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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diff changeset
17 #such as with hg19 above.
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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18 #
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta