Got a fair bit of experience submitting cellprofiler jobs to a SGE cluster at my old group, it’s not exactly simple and a lot of it will be specific to your setup.
The general idea was to generate a csv file per task that was suitable for the LoadData module, and then create a cellprofiler command per task in a plain text file, then loop through these lines as an SGE array job with the
The other approach is to have one big csv file suitable for LoadData, and use the cellprofiler commands with the
-l flags, although I found Cellprofiler isn’t a fan of huge files for LoadData.
There’s python program here to automate the process on our setup, which might give you some ideas.