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PNNL-CompBio / decomprolute

A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
MIT License
15 stars 4 forks source link

Make the cibersortx dockers works in the workflow #32

Closed LifeWorks closed 3 years ago

LifeWorks commented 3 years ago

Currently, mcpcounter and xcell docker containers work well in the workflow. Need to bring cibersortx in.

LifeWorks commented 3 years ago

Problem with cibersort: It has designated directories for using the docker image

Usage: docker run cibersortxfractions [Options]

Bind Mounting: 2 directories must be bind mounted to be accessed within the docker container: 1) Input file dir

Format: -v {dir_path}:/src/data 2) Outdir Format: -v {dir_path}:/src/outdir Note: Absolute paths required

sgosline commented 3 years ago

Closed with#42