Documentation not up to date?!

cellprofiler

#1

hi,

i am not sure, but i have the feeling that the CellProfiler documentation and the actual code are not completely synchronized at the moment.

i feel that the documentation tells one to create a batchrun.sh file that would access a series of .mat files,
whereas the actual implementation is rather to use batchrunner.py which actually creates that different jobs…

is that correct?!

thanks,
christian.


#2

Thanks for reporting this. Indeed, the BatchProcessing help in Help->General Help is old. The Help for the CreateBatchFiles module is more up-to-date, and that is perhaps the case for other modules vs. general Help. We’ll check on that.

Yes, we are now using BatchRunner.py to execute our batch runs at the command-line. Note that there is also a SubmitBatch DataTool that is GUI-driven, however it requires a webserver to be setup to access the files and some of the code would need to be tailored to your setup, e.g. specific URLs and folders where the CPCluster executable resides.

David