My scope is fitted with a 2.5" Moonlite focuser. To automate focusing I have a Pegasus Astro Motor Focus. This connects via a serial cable directly to my Pegasus Astro Ultimate Powerbox. Focus is controlled by Sequence Generator Pro (SGP)

 

I have SGP set up to focus at the start of a sequence and on every filter change. I've also set it so that it autofocuses every hour if auotfocus hasn't been triggered by a filter change.

Sequence Generator Pro autofocus in action. This software in increments of 100 steps in my case, a 10 second photograph is taken and a calculation performed to work out the HFR (Half Flux Radius) a measure of how sharp the stars are in the image. The results of focus position and HFR is plotted and the sharpest focus is the low point of the curve. The focuser is set to this position before the sequence starts (or continues)