In Geneious Prime 2022 onwards, you can run Geneious operations from the command line.
To use the command line interface (CLI), you must have a licensed copy of Geneious installed on the machine. Your license must have been activated either in the GUI interface, or by configuring the geneious.properties file (see section 22.2.2 ) prior to using the CLI. You must also install any plugins you wish to use via the Plugins menu in the GUI interface.
On Windows and Linux, no further configuration is required to run the CLI after installation of Geneious, just open the Command Prompt or Terminal and type geneious to run it.
On macOS you must create symlinks yourself so that the geneious command can be run from any directory in the Terminal.
To do this, use the following command:
sudo ln -sf /Applications/Geneious Prime.app/Contents/Resources/app/resources/geneious /usr/local/bin
(this assumes Geneious is installed in the default location in Applications)
Note that sudo (admin) privileges are required to create the symlink. However once this is created, the geneious CLI can be run by non-admin users.