Installation and Dependecies

Installation

Dependencies

Ensure you have the following dependencies in your PATH. We list the version numbers that we used in development, but other versions of these dependencies will likely work fine.

BASH environment 
bedtools v2.29.0 (for intersectBed)
cooler v0.9.3 (if using .mcool files)
python3 v3.7.3

Required Python packages

hicstraw v1.3.0 (if working with .hic files)
numpy v1.21.6
scipy v1.7.3
statsmodels v0.13.2
tqdm v4.19.6

After these dependencies are installed, simply clone the repository or download the release.

To run CRUSH, you may want to make the tool directly executable. e.g. sudo chmod +x CRUSH/CRUSH_v1.0 and/or add to your PATH. Then try: CRUSH/CRUSH_v1.0 --help