Config file options

Config file

There are configuration details you can add to a job:

• experiment : path to an ImageXpress experiment
• chunk number of imagesets per job
• pipeline : path to a cellprofiler pipeline
• location : path to where to store the loaddata modules, staged data and output
• commands location : path to where to store the qsub array commands
• remove plate : plate names in experiment to be removed
• add plate :
  • experiment : path to another ImageXpress experiment
  • plates : plate name(s) in the above experiment

i.e we could remove some plates from an experiment, and also include some plates from a different experiment

experiment: /path/to/imageXpress/experiment

# remove two plates from current experiment
remove plate:
    - plate_1
    - plate_2

# add plates from a separate experiment
add plate:
    - experiment : /path/to/different/experiment
    - plates:
        - plate_exp2_1
        - plate_exp2_2

chunk: 96

pipeline: /pipelines/pipeline_1.cppipe

location: /path/to/scratch/space

commands location: /path/to/scratch space

We can also use add plate without the an experiment tag to add a few plates from a large experiment.

add plate:
    - experiment: /path/to/large/experiment
    - plates:
        - plate_1
        - plate_2
        - plate_3
chunk : 46
pipeline : /path/to/cellprofiler/pipeline.cppipe
location : /path/to/scratch/space
commands location : /home/user