Installation

Conda

# install mamba
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh

# create a conda environment and install the required packages
conda create --name pigeon_feather python=3.11
conda activate pigeon_feather

conda install jupyterlab mdanalysis numba
conda install pymol-open-source

pip install pyopenms hdxrate

# clone the PIGEON-FEATHER repo
git clone https://github.com/glasgowlab/PIGEON-FEATHER.git

# clone the bayesian hdx iso repo
git clone https://github.com/lucl13/bayesian_hdx.git

cd PIGEON-FEATHER
pip install .

cd ../bayesian_hdx
pip install .

Docker

docker build -f docker/Dockerfile -t pigeon_feather:0.9 .
docker run -it -v $(pwd):/work -p 8889:8889 --rm pigeon_feather:0.9 jupyter-lab --port 8889

To open the Jupyter notebook, please click the link displayed in the terminal. For users operating on Apple Silicon machines, it may be necessary to append –platform amd64 when building the image, as pyopenms is not supported on the linux/arm64 architecture. It is advisable to avoid running the Docker container on Apple Silicon machines due to the significant performance degradation caused by the emulation of the x86_64 architecture.

Note: bayesian_hdx at the above link is a fork of the original repo , which has been modified for compatibility with the PIGEON-FEATHER workflow and support for isotopic envelope fitting.