Usage via command line

The pipeline provides a command line tool cellmaps_pipelinecmd.py that can run the pipeline serially or in parallel via SLURM For more information run the following:

The example below runs the pipeline using example data. This may take up to an hour to run.

cellmaps_pipelinecmd.py myexample_run --samples examples/samples.csv \
                        --unique examples/unique.csv \
                        --edgelist examples/edgelist.tsv \
                        --baitlist examples/baitlist.tsv \
                        --provenance examples/provenance.json \
                        --ppi_cutoffs 0.01 0.1

Note

Above assumes the repo has been cloned locally and the command above is run within the base directory of the repo