Command Line Interface
bioregistry automatically installs the command bioregistry. See
bioregistry --help for usage details.
bioregistry
Run the Bioregistry CLI.
bioregistry [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
align
Align all external registries.
bioregistry align [OPTIONS]
Options
- --skip-fairsharing
- --skip-re3data
- --skip-slow
- --no-force
compare
Compare the registries.
bioregistry compare [OPTIONS]
export
Export the Bioregistry.
bioregistry export [OPTIONS]
lint
Run the lint commands.
bioregistry lint [OPTIONS]
update
Update the Bioregistry.
bioregistry update [OPTIONS]
web
Run the web application.
bioregistry web [OPTIONS]
Options
- --host <host>
Flask host.
- Default:
0.0.0.0
- --port <port>
Flask port.
- Default:
5000
- --with-gunicorn
Use gunicorn instead of flask dev server
- --workers <workers>
Number of workers
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --registry <registry>
Path to a local registry file
- --metaregistry <metaregistry>
Path to a local metaregistry file
- --collections <collections>
Path to a local collections file
- --contexts <contexts>
Path to a local contexts file
- --config <config>
Path to a configuration file
- --base-url <base_url>
Base URL for app
- Default:
https://bioregistry.io