Installation

The GraphST package is developed based on the pytorch framework and can be implemented on both GPU and CPU. We recommend running the package on GPU. Please ensure that pytorch and CUDNN are installed correctly. To run GraphST, all dependencies included in the file ‘requirement.txt’ need to be installed. We provide two ways to install the package of GraphST.

Please note that the current GraphST version offers full support of Linux operating system. Further version for other operating systems would be released soon.

1. Python

Dowloading the package from https://github.com/JinmiaoChenLab/GraphST/

pip install GraphST

or

git clone https://github.com/JinmiaoChenLab/GraphST.git

cd GraphST

python setup.py build

python setup.py install --user

2. Anaconda

For convenience, we suggest using a separate conda environment for running GraphST. Please ensure annaconda3 is installed.

Create conda environment and install GraphST package.

#create an environment called GraphST
conda create -n GraphST python=3.8

#activate your environment
conda activate GraphST

#install package

pip install GraphST

or

git clone https://github.com/JinmiaoChenLab/GraphST.git

cd GraphST

python setup.py build

python setup.py install --user

#To use the environment in jupyter notebook, add python kernel for this environment.

pip install ipykernel

python -m ipykernel install --user --name=GraphST