ENCODE methylation pipeline for command line

Question

[ccagg]

Hi,

Does anyone know of an implementation of the ENCODE WGBS pipeline for the command line? I am familiar with the DNAnexus implementation and this implementation, https://github.com/ENCODE-DCC/dna-me-pipeline , however, I cannot get the above to work on our lab's cluster

The pipeline I am referring to is this https://www.encodeproject.org/wgbs/

Thanks!