README.md

HMC Benchmark

NOTE: this pipeline is a work in progress and hasn't undergone much testing!

1. Install requirements (python 3.6!)

conda env create -f environment.yml

2. Activate environment and export environment variables:

source activate hmc
export PYTHONPATH=$PYTHONPATH:./code/
export PATH=$PATH:./code/

3. Run pipeline via snakemake:

# Inspect commands to be run via dry-run:
snakemake -np

# Run the pipeline (local mode):
snakemake -p

Cluster based parallelization is also available via, e.g., snakemake --cluster="qsub ......" The details of the pipeline are the rules in Snakefile.