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 (when using –with-gunicorn)
- Default:
5
- -v, --verbose¶
Enable verbose mode. More -v’s means more verbose.
- --timeout <timeout>¶
The timeout used for gunicorn
- --debug¶
Run flask dev server in debug mode (when not using –with-gunicorn)
- --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