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)