MegaQC Commandline Interface


Welcome to the MegaQC command line interface.

See below for the available commands - for example,

to start the MegaQC server, use the command: megaqc run




Show the flask version


Show all registered routes with endpoints and methods.

megaqc routes [OPTIONS]


-s, --sort <sort>

Method to sort routes by. “match” is the order that Flask will match routes when dispatching a request.




Show HEAD and OPTIONS methods.


Run a local development server.

This server is for development purposes only. It does not provide the stability, security, or performance of production WSGI servers.

The reloader and debugger are enabled by default if FLASK_ENV=development or FLASK_DEBUG=1.

megaqc run [OPTIONS]


-h, --host <host>

The interface to bind to.

-p, --port <port>

The port to bind to.

--cert <cert>

Specify a certificate file to use HTTPS.

--key <key>

The key file to use when specifying a certificate.

--reload, --no-reload

Enable or disable the reloader. By default the reloader is active if debug is enabled.

--debugger, --no-debugger

Enable or disable the debugger. By default the debugger is active if debug is enabled.

--eager-loading, --lazy-loader

Enable or disable eager loading. By default eager loading is enabled if the reloader is disabled.

--with-threads, --without-threads

Enable or disable multithreading.

--extra-files <extra_files>

Extra files that trigger a reload on change. Multiple paths are separated by ‘:’.


Run an interactive Python shell in the context of a given Flask application. The application will populate the default namespace of this shell according to it’s configuration.

This is useful for executing small snippets of management code without having to manually configure the application.

megaqc shell [OPTIONS]