Installation¶
Prerequisites¶
conda prerequisites¶
Install Conda. We typically use the Miniconda Python distribution. Use Python version >=3.7.
Create a new conda environment:
conda create -n scgen-env python=3.7
Activate your environment:
source activate scgen-env
pip prerequisites:¶
Install Python, we prefer the pyenv version management system, along with pyenv-virtualenv.
Install PyTorch. If you have an Nvidia GPU, be sure to install a version of PyTorch that supports it – scGen runs much faster with a discrete GPU.
scGen installation¶
Install scgen in one of the following ways:
Through pip:
pip install scgen
Through pip with packages to run notebooks. This installs scanpy, etc.:
pip install scgen[tutorials]
Nightly version - clone this repo and run:
pip install .
For development - clone this repo and run:
pip install -e .[dev,docs]