scArches requires Python 3.7 or 3.8. We recommend to use Miniconda.
The easiest way to get scArches is through pip using the following command:
sudo pip install -U scarches
You can also use our environment file. This will create the conda environment ‘scarches’ with the required dependencies:
git clone https://github.com/theislab/scarches cd scarches conda env create -f envs/scarches_linux.yml conda activate scarches
You can also get the latest development version of scArches from Github using the following steps:
First, clone scArches using
git clone https://github.com/theislab/scarches
cd to the scArches folder and run the install command:
cd scarches python3 setup.py install
On Windows machines you may need to download a C++ compiler if you wish to build from source yourself.
The list of dependencies for scArches can be found in the requirements.txt file in the repository.
If you run into issues, do not hesitate to approach us or raise a GitHub issue.