I’m trying to run CP4 from command line, I have a docker container that works well and I’m passing a pipeline file (attached) that (should) load tiff files using the LoadData module.
the code I use is:
cellprofiler --run \ --run-headless \ --pipeline plugins/segmentation_load_data.cppipe \ --data-file list_files.csv \ --plugins-directory plugins/cp_plugins \ --output-directory results/CP4_test_res \ --log-level DEBUG
the csv file is attached too.
basically markers are analyzed separately and I need to call each marker at different points in the pipeline.
I used the
Image_Filename_xxx format, where
xxx is the name of the marker like
Image_Filename_CD8a to indicate
CD8a markers, respectively.
then I used
1 to indicate what marker is what and the GUI version actually does pass the correct name to the correct module.
however when I run it from command line, what I get is the following error:
FileNotFoundError: [Errno 2] The file, /mnt/lustre/users/SBata/0 , does not exist.
so it seems to me that CP is not using the
1s to select markers, but it’s taking it as a path and looking for that folder.
I looked at a few posts here but I could not find any answer.
any help would be great.