Mercurial > repos > iuc > data_manager_star_index_builder
annotate tool-data/all_fasta.loc.sample @ 12:71c994a11f71 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author | iuc |
---|---|
date | Thu, 05 Dec 2024 06:49:40 +0000 |
parents | cdc4d8a998e1 |
children |
rev | line source |
---|---|
0
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
1 #This file lists the locations and dbkeys of all the fasta files |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
2 #under the "genome" directory (a directory that contains a directory |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
3 #for each build). The script extract_fasta.py will generate the file |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
4 #all_fasta.loc. This file has the format (white space characters are |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
5 #TAB characters): |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
6 # |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
0
diff
changeset
|
7 #<unique_build_id> <dbkey> <display_name> <file_path> |
0
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
8 # |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
10 # |
1
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
0
diff
changeset
|
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
0
diff
changeset
|
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
cdc4d8a998e1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
0
diff
changeset
|
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
0
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
14 # |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
15 #Your all_fasta.loc file should contain an entry for each individual |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
16 #fasta file. So there will be multiple fasta files for each build, |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
17 #such as with hg19 above. |
e4b87a00b1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c-dirty
iuc
parents:
diff
changeset
|
18 # |