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cptools2

Setting up CellProfiler jobs to run on eddie3.

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Installation

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.

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CellProfiler pipline

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Creating a config file

cptools2 uses a config file which details:

• An ImageXpress experiment directory to analyse
• (optional) which selected plates from that experiment to include or exclude
• The number of imagesets to be analysed in each eddie job
• The CellProfiler pipeline to be used
• The location to store the results

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/commands

More examples here (make a separate page for the config file options)

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Creating commands from the config file

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Creating submission scripts

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Submitting jobs

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