Mercurial > repos > iuc > data_manager_hisat2_index_builder
annotate test-data/all_fasta.loc @ 6:a04cebcd77f4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:49:53 +0000 |
| parents | 8eac26f44d29 |
| children |
| rev | line source |
|---|---|
|
5
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
1 #This file lists the locations and dbkeys of all the fasta files |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
2 #under the "genome" directory (a directory that contains a directory |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
3 #for each build). The script extract_fasta.py will generate the file |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
4 #all_fasta.loc. This file has the format (white space characters are |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
5 #TAB characters): |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
6 # |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
7 #<unique_build_id> <dbkey> <display_name> <file_path> |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
8 # |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
10 # |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
14 # |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
15 #Your all_fasta.loc file should contain an entry for each individual |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
16 #fasta file. So there will be multiple fasta files for each build, |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
17 #such as with hg19 above. |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
18 # |
|
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
diff
changeset
|
19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |