annotate tool-data/all_fasta.loc.sample @ 3:ac048a34cac3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit 7224953c0b42f43a91dc76ee1015f355a311b391"
author iuc
date Fri, 12 Feb 2021 12:55:56 +0000
parents 70efe7b19018
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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2 #under the "genome" directory (a directory that contains a directory
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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3 #for each build). The script extract_fasta.py will generate the file
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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5 #TAB characters):
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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6 #
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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8 #
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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9 #So, all_fasta.loc could look something like this:
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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10 #
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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14 #sars-cov-2 SARS-CoV-2 SARS-CoV-2 (MN908947.3) /depot/data/MN908947_3_Wuhan-Hu-1.fasta
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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15 #
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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16 #Your all_fasta.loc file should contain an entry for each individual
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
iuc
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17 #fasta file. So there will be multiple fasta files for each build,
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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18 #such as with hg19 above.
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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19 #
70efe7b19018 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
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20 #