In Geneious Prime 2022 onwards you can run Geneious Prime operations via the command line rather than the graphical interface (GUI).
How to access the command line interface (CLI)
To use the CLI you must have a licensed copy of Geneious Prime installed on the machine. Your license must have been activated either in the GUI interface, or by configuring the geneious.properties file (see Advanced Administration chapter of the Geneious User Manual) 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 Prime, 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 Prime 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.
How to run operations via the CLI
Geneious Prime operations in the CLI follow the basic format
geneious -i <input_file_name> --operation <operation_name> <-options> -o <output_file_name>
To see all available operations, type
geneious --list
(add --filter <operation type> to filter the list on specific types of operations)
To see all options for a given operation, type
geneious --options-for <operation>
(add --advanced to see advanced options)
To see some examples of how to use the CLI, type
geneious --examples
From Geneious Prime 2022.2 onwards, the CLI can use files directly from your local or shared database. In prior versions, files for input to the CLI needed to be exported from the Geneious database so they were stored as files on your drive.
To use documents from your local or shared database as input to a CLI command, add the name of the database followed by a :, and then the path to the file. The local database is always called Local. For example, to use a document from the local database, use:
-i "Local:folder/folder/document"To use a document from a Shared database use:
-i "my_shared_database:folder/folder/document"my_shared_database is your Shared Database name, and folder/folder/document is the path to your file in Geneious)
For more examples of how to push and pull files from the Geneious database to the command line, please see the Geneious User Manual.
The CLI can also be used with an options profile file or Geneious workflow file to simplify setting algorithm options and automating tasks in the CLI. Please see Command Line Interface chapter of the Geneious User Manual for further instructions.
The command line interface is under active development. If you would like to see additional functionality or have any comments regarding it, please contact support.