Running conversion processes on a headless linux machine

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Summary of the problem or suggestion:

Would it be possible ( with some custom code )? to run the ffmpeg (or handbrake) processes on a linux machine? But have those conversion jobs handled by an instance of MceBuddy running on windows?

I’ve got a quandro p2000 in my plex server running on Ubuntu, and given that it can transcode video lightning fast, I’d like to leverage that capability to convert my recordings.

Is this possible somehow? What would be required to make it happen?

Thanks Goose.