Installation¶

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
```

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.

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]