Code used to generate the Complex Medically Relevant Genes benchmark sets.
Pipeline dependencies are available as conda packages, including jupyter notebook with a bash kernel to run the pipeline in the jupyter notebooks. The required packages are are defined inenvironment.yml.
Create the conda env (can also use mamba, a faster implementation of the conda package manager).
conda env create --name cmrg_benchset --file environment.yml
Pipelines are run in ipython notebooks using the bash kernel
conda activate cmrg_benchset
## Use ipython notebook for bash kernel
ipython notebook