General options

Nebulizer supports a number of general options for managing how connections are made to Galaxy servers, how to authenticate, and what information to output.

Authenticating without stored credentials

Use --api_key (-k) to explicitly specify the API key to use for authentication on the command line, e.g.

nebulizer -k API_KEY COMMAND...

Use the --username (-u) option to authenticate using the normal Galaxy login credentials (i.e. email and password) instead of the API key, e.g.

nebulizer -u USER@DOMAIN COMMAND...

You will be prompted to enter the password, but you can also use the --galaxy_password (-P) option to specify it explicitly on the command line.

Controlling warnings and debugging output

--suppress-warnings (-q) suppresses warning messages from Nebulizer; conversely debugging output can be enabled using the --debug option.

Handling SSL certificate verification failures

Nebulizer commands will fail for Galaxy instances which are served over https protocol without a valid SSL certificate, reporting an error like:

[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590), 0 attempts left: None

In this case adding the --no-verify (-n) option turns off the certificate verification and should enable a connection to be made.