Mercurial > repos > jjohnson > eggnog_mapper_data_manager
comparison tool-data/eggnog_mapper_db.loc.sample @ 0:2909815b6a01 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
| author | jjohnson |
|---|---|
| date | Thu, 07 Nov 2019 12:41:50 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:2909815b6a01 |
|---|---|
| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of eggnog_mapper data files. | |
| 3 # | |
| 4 # eggnog-mapper requires the following files to be installed in the data directory: | |
| 5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz | |
| 6 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz | |
| 7 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz | |
| 8 # In addition individual HMM DBs can be installed from: | |
| 9 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ | |
| 10 # A complete diamond database is available from: | |
| 11 # http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz | |
| 12 # | |
| 13 # The python script download_eggnog_data.py, | |
| 14 # included with eggnog_mapper, can be used to download the files to the correct directory | |
| 15 # | |
| 16 # The near-equivalence of columns "value" and "db" is needed for the tests to work, | |
| 17 # and for the setting of --data_dir to the parent directory of eggnog.db | |
| 18 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. | |
| 19 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases | |
| 20 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, | |
| 21 # value and db should be the same (in the example, both should be "thaNOG") | |
| 22 # | |
| 23 # | |
| 24 #db_version name path | |
| 25 #4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db |