Install Python 3.7. We typically use the Miniconda Python distribution and Linux.
Install PyTorch. If you have an Nvidia GPU, be sure to install a version of PyTorch that supports it – scVI runs much faster with a discrete GPU.
Install scVI in one of the following ways:
conda install scvi -c bioconda -c conda-forge
pip install scvi
Through pip with packages to run notebooks. This installs scanpy, etc.:
pip install scvi[notebooks]
Nightly version - clone this repo and run:
pip install .
For development - clone this repo and run:
pip install -e .[test,notebooks]
If you wish to use multiple GPUs for hyperparameter tuning, install MongoDb.