Mercurial > repos > iuc > crossmap_bam

annotate tool-data/all_fasta.loc.sample @ 3:cb3557cabc7b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:10:46 -0400
parents d04d5afec2e0
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d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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2 #under the "genome" directory (a directory that contains a directory
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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3 #for each build). The script extract_fasta.py will generate the file
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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5 #TAB characters):
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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6 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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8 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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9 #So, all_fasta.loc could look something like this:
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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10 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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14 #
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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17 #such as with hg19 above.
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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18 #