Installation

A conda virtual environment is highly recommended when training Steamboat. After you are at the root path of this directory, use the following commands to set up a proper virtual environment:

conda create -n steamboat python=3.11
conda activate steamboat

To use CUDA for model fitting, follow the instructions to install PyTorch.

You can then use pip to install Steamboat and all the dependencies:

git clone https://github.com/ma-compbio/Steamboat.git
cd Steamboat
git install .