Mercurial > repos > bgruening > data_manager_diamond_database_builder
annotate test-data/diamond_database.loc @ 1:5a0d0bee4f8d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
| author | bgruening |
|---|---|
| date | Tue, 03 Dec 2019 17:39:48 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
|
1
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
1 #This file lists the locations and dbkeys of all the fasta files |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
2 #under the "genome" directory (a directory that contains a directory |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
3 #for each build). The script extract_fasta.py will generate the file |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
4 #all_fasta.loc. This file has the format (white space characters are |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
5 #TAB characters): |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
6 # |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
7 #<unique_build_id> <dbkey> <display_name> <file_path> |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
8 # |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
10 # |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
14 # |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
15 #Your all_fasta.loc file should contain an entry for each individual |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
16 #fasta file. So there will be multiple fasta files for each build, |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
17 #such as with hg19 above. |
|
5a0d0bee4f8d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents:
diff
changeset
|
18 # |