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-bioportal

--skip-agroportal

--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'