Mercurial > repos > iuc > jvarkit_wgscoverageplotter
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 | 
| rev | line source | 
|---|---|
| 2 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 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 parents: diff
changeset | 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 parents: diff
changeset | 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 parents: diff
changeset | 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"
 iuc parents: diff
changeset | 5 #TAB characters): | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 6 # | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 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 parents: diff
changeset | 8 # | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 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"
 iuc parents: diff
changeset | 10 # | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 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 parents: diff
changeset | 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 parents: diff
changeset | 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"
 iuc parents: diff
changeset | 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"
 iuc parents: diff
changeset | 15 # | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 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 parents: diff
changeset | 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"
 iuc parents: diff
changeset | 18 #such as with hg19 above. | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 19 # | 
| 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 iuc parents: diff
changeset | 20 # | 
