How to run Geneious operations via the command line

In Geneious Prime 2022 onwards you can run Geneious 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 installed on the machine. Your license must have been activated either in the GUI interface, or by configuring the file (see section 22.4 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, 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\ /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.

How to run operations via the CLI

Geneious 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)


Note that the command line interface cannot currently access files directly from your Geneious data folder.  If you have files currently in Geneious you want to use as input to operations in the CLI, you must export them from geneious so that they are stored as files on your drive.  They can be exported in either .geneious format or any of the common sequence formats.  You can also use raw sequence files (such as fastq files from your sequencing provider) that have not been imported into Geneious.  

To see some examples of how to use the CLI, type

geneious --examples


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 sections 21.3 and 21.4 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.

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