Run this docker image using the following command:
docker run -it -v /path/to/my/data:/commwalker/data lueckenmd/commwalker
Note that the data folders should not have trailing slashes! The folder specified should contain all the data on which you want to run the algorithm, including functional similarity matrix and network edgelist. All output files should be stored in the /commwalker/data folder for them to be accessible outside of the docker container.
A test of commwalker can also be run without a mounted volume using the example data via the command:
docker run -it lueckenmd/commwalker
The README for this algorithm is found in a tarball at opig.stats.ox.ac.uk/resources.
Please cite CommWalker via the following publication:
Luecken MD, Page, MJT, Crosby AJ, Mason S, Reinert G, Deane CM, CommWalker: Correctly Evaluating Modules in Molecular Networks in Light of Annotation Bias, Bioinformatics (under review)