Installation

Requirements

Note: The current version of SPACEL only supports Linux and MacOS, not Windows platform.

To install SPACEL, you need to install PyTorch with GPU support first. If you don’t need GPU acceleration, you can just skip the installation for cudnn and cudatoolkit.

• Create conda environment for SPACEL:

conda env create -f environment.yml

or

conda create -n SPACEL -c conda-forge -c default cudatoolkit=10.2 python=3.8 rpy2 r-base r-fitdistrplus

You must choose correct PyTorch, cudnn and cudatoolkit version dependent on your graphic driver version.

Note: If you want to run 3D expression GPR model in Scube, you need to install the Open3D python library first.

Installation

• Install SPACEL:

pip install SPACEL

• Test if PyTorch for GPU available:

python
>>> import torch
>>> torch.cuda.is_available()

If these command line have not return True, please check your gpu driver version and cudatoolkit version. For more detail, look at CUDA Toolkit Major Component Versions.