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Setting up CellProfiler jobs to run on eddie3.
cptools2 automatically creates commands for eddie3 array jobs, and csv files suitable for CellProfiler LoadData module.
Make sure you're on a worker node, then load python2.7 with module load python.
Go to the cptools2 location (/exports/igmm/eddie/Drug-Discovery/tools/cptools2)
When you're within the cptools2 directory you will see a file called setup.py.
Install with python setup.py install --user.
The cellprofiler pipelines need to be set up in a certain way to be used with cptools2.
The pipeline should start with a LoadData module, which takes the image information in the form of a csv file which is produced by cptools2.
It's easier to create the pipeline using the normal drag-and-drop interface in cellprofiler to load the images, and extracting metadata from the file paths. Then at the end change it to use the LoadData module.
Channels names in the cellprofiler pipeline need to be W and then numbered, so W1, W2 ... etc.
The pipelines should end with an ExportToSpreadsheet module, with the location set to Elsewhere.
cptools2 uses a config file which details:
- The ImageXpress experiment to analyse
- If certain plates should be included/excluded
- How many imagesets should each job analyse
- The CellProfiler pipeline to use
- Where to save the results
- Where to save the submission commands
An example of a config file:
experiment: /path/to/ImageExpress/experiment
chunk: 96
pipeline: /path/to/cellprofiler/pipeline.cppipe
location: /path/to/output/location
commands location: /where/to/store/commandsMore details on config file options
To create the commands and LoadData csv files, first make sure you're on a staging node with access to datastore.
Then, if you're in the cptools2 directory:
python -m cptools2 /path/to/config.yml
Where config.yml is your configuration file.
This should create the staging, analysis, and destaging commands in the commands location. And, creates a LoadData csv file for each job in the location directory.