Study by Timothy Yu and Jesse Bloom.

Build the conda environment using the provided environment.yml file in this directory:

conda env create -f environment.yml 

Some of the analyses are automated by snakemake. To run the pipeline:

conda activate ha-epistasis
snakemake -j 8 -s Snakefile --rerun-incomplete

To run on the Hutch cluster via slurm, you can run:

sbatch -c 8 run_hutch_cluster.bash

Note some parts of the analysis depend on a local installation of ChimeraX. The files in data/rmsd were pre-generated so that the pipeline runs in a single go, but they depend on files generated in the pipeline. If you'd like to reproduce them, open the ChimeraX scripts rmsd_ha1.cxc and rmsd_ha2.cxc in ChimeraX.

This pipeline builds HTML documentation in ./docs/. These docs are rendered for viewing at https://jbloomlab.github.io/ha-preference-shifts/.