Installation#

scArches requires Python 3.7 or 3.8. We recommend to use Miniconda.

PyPI#

The easiest way to get scArches is through pip using the following command:

sudo pip install -U scarches

Conda Environment#

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.yaml
conda activate scarches

Development#

You can also get the latest development version of scArches from Github using the following steps: First, clone scArches using git:

git clone https://github.com/theislab/scarches

Then, 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.

Dependencies#

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.