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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. Note that 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. Geneious –examples Using files from your local or shared database with the CLIįrom Geneious Prime 2022.2 onwards, the command line interface can be used directly on files in your Geneious database.
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To see some examples of how to use the CLI, type Geneious –options-for (add –advanced to see advanced options) To see all options for a given operation, type Geneious –list (add –filter to filter the list on specific types of operations) Geneious operations in the CLI follow the basic format: However once this is created, the geneious CLI can be run by non-admin users.
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Note that sudo (admin) privileges are required to create the symlink. (this assumes Geneious is installed in the default location in Applications) Sudo ln -sf /Applications/Geneious Prime.app/Contents/Resources/app/resources/geneious /usr/local/bin On macOS you must create symlinks yourself so that the geneious command can be run from any directory in the Terminal. 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. You must also install any plugins you wish to use via the Plugins menu in the GUI interface. Your license must have been activated either in the GUI interface, or by configuring the geneious.properties file prior to using the CLI. To use the command line interface (CLI), you must have a licensed copy of Geneious installed on the machine.
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In Geneious Prime 2022 onwards, you can run Geneious operations from the command line. Command Line Interface Running Geneious Prime operations from the command line