The methods and experiments are written in Python 3. We recommend using Conda to manage dependencies, which you can do directly using the provided environment.yml file:
conda env create -f environment.yml
source activate hubalign-py-env
Note that HubAlign requires a C++ compiler. Consequently, we include the Conda gxx_linux_64 as a dependency in the environment.yml. You may need to update or remove this dependency if you are on a non-Linux system.