Mercurial > repos > matthias > data_manager_bowtie2_index_builder

annotate tool-data/all_fasta.loc.sample @ 0:68fd790f3916 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 eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
author matthias
date Thu, 02 Apr 2020 13:16:53 +0000
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68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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1 #This file lists the locations and dbkeys of all the fasta files
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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2 #under the "genome" directory (a directory that contains a directory
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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3 #for each build). The script extract_fasta.py will generate the file
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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4 #all_fasta.loc. This file has the format (white space characters are
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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5 #TAB characters):
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
parents:
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6 #
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
parents:
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8 #
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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9 #So, all_fasta.loc could look something like this:
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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10 #
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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14 #
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
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15 #Your all_fasta.loc file should contain an entry for each individual
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
parents:
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17 #such as with hg19 above.
68fd790f3916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
matthias
parents:
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18 #