I think I am following you - please bear with me if I am not .
It sounds to me as though you should just dispense with the cluster version of CellProfiler and “Batch processing” altogether. You ought to be able to simply:
On the Local machine, with the Windows Binary version (since no Matlab):
(1) Create your pipeline on the local machine
(2) Save the pipeline (File->Save Pipeline)
(3) Manually move the .mat file to the Windows server
On the server, with the Windows Binary,
(4) Load .mat
(5) Run it.
No need for CreateBatchFiles Module at all, especially since there is only one server computer. And note that you would not need CPCluster - this is only for computing clusters that read in output files broken up into separate batch output .mat files by a CreateBatchFiles Module.
Perhaps the confusion is in the term “batch processing”? The standalone CellProfiler can load in multiple files and process each one through a pipeline, and only if you have an inordinate amount of images would you need to break up your overall job into separate jobs and send them off to a cluster of machines (our usage of “batch”).
One thing I don’t understand is your usage of “batchone.m” - do you mean batchone.mat"? The output files are .mat.
As for the MCR installer problem, are you logged in as an administrator? I just installed MCR with my laptop and it worked fine (after a reboot, that is). If this isn’t it, then I’ll have to ask around here. And you should not be using the CPCluster version as your primary CellProfiler program.
Let me know if this isn’t clear, or if it still doesn’t apply to your situation.