databases.py
usage: databases.py
Main script to configure Autometa database dependencies.
optional arguments:
-h, --help show this help message and exit
--config CONFIG </path/to/input/database.config> (default:
DEFAULT_FPATH)
--dryrun Log configuration actions but do not perform them.
(default: False)
--update-all Update all out-of-date databases. (NOTE: Does not
update GTDB) (default: False)
--update-markers Update out-of-date markers databases. (default: False)
--update-ncbi Update out-of-date ncbi databases. (default: False)
--update-gtdb Download and format the user-configured GTDB release
databases (default: False)
--check-dependencies Check database dependencies are satisfied. (default:
False)
--no-checksum Do not perform remote checksum comparisons to validate
databases are up-to-date. (default: False)
--nproc NPROC num. cpus to use for DB formatting. (default: 2)
--out OUT </path/to/output/database.config> (default: None)
By default, with no arguments, will download/format databases into default
databases directory.