Mercurial > repos > iuc > data_manager_bowtie_index_builder

annotate tool-data/all_fasta.loc.sample @ 7:a601bb53be5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author iuc
date Thu, 05 Dec 2024 06:47:05 +0000
parents 00d807711b52
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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2 #under the "genome" directory (a directory that contains a directory
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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3 #for each build). The script extract_fasta.py will generate the file
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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5 #TAB characters):
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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6 #
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00d807711b52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 88ce6b707389753fa419f5abe469c6c7b0de0570
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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diff changeset
8 #
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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9 #So, all_fasta.loc could look something like this:
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
parents:
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10 #
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00d807711b52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 88ce6b707389753fa419f5abe469c6c7b0de0570
iuc
parents: 0
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
00d807711b52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 88ce6b707389753fa419f5abe469c6c7b0de0570
iuc
parents: 0
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
00d807711b52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 88ce6b707389753fa419f5abe469c6c7b0de0570
iuc
parents: 0
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
parents:
diff changeset
14 #
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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17 #such as with hg19 above.
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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diff changeset
18 #