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.