For a command line program to be integrated using the plugin wrapper system (download here), it must at least meet the following requirements:
- Accepts input sequences as files on disk in a format that Geneious Prime can export.
- Produces output as files on disk in a format that Geneious Prime can import. Note that Geneious can import a plain text file as a way to handle small report-like files. Standard output can be redirected to a file on disk using ">" if the program doesn't have the option to write to a file.
- Can be executed as a single command. Programs that require multiple commands such as indexing before running are not supported.
- Doesn't require any interaction while running. Any prompts on the command line or any GUI are not supported.
- If the plugin is to be distributed to others with a copy of the program bundled, it should be completely portable. e.g. Statically linked dependencies, no python or other runtimes required.
- The wrapper plugin system can only save results as new documents in Geneious, it cannot be used to edit or annotate existing documents.
For more complicated integrations, the Plugin Development Kit must be used.