If you do not have a working installation of Python 3.6 (or later), consider installing Miniconda (see [Installing Miniconda]). Then run:
conda install -c conda-forge scanpy python-igraph leidenalg
Pull Scanpy from PyPI (consider using
pip3 to access Python 3):
pip install scanpy
If you prefer to exclusively use PyPI run:
pip install 'scanpy[leiden]'
[leiden] installs two packages that are needed for popular
parts of scanpy but aren’t requirements: python-igraph [^cite_csardi06] and leiden [^cite_traag18].
To work with the latest version on GitHub: clone the repository and
cd into its root directory.
gh repo clone scverse/scanpy cd scanpy
If you are using
pip>=21.3, an editable install can be made:
pip install -e '.[dev,doc,test]'
For older versions of
pip, flit can be used directly.
To install using symbolic links (stay up to date with your cloned version after you update with
git pull) call:
flit install -s --deps=develop # from an activated venv or conda env # or flit install -s --deps=develop --python path/to/venv/bin/python
If you want to let [conda] handle the installations of dependencies, do:
pip install beni beni pyproject.toml > environment.yml conda env create -f environment.yml conda activate scanpy flit install -s --deps=develop
On Windows, you might have to use
flit install --pth-file
if you are not able to give yourself the create symbolic links privilege.
For instructions on how to work with the code, see the contributing guide.
If you’re using Docker, you can use e.g. the image gcfntnu/scanpy from Docker Hub.
If you get a
Permission denied error, never use
sudo pip. Instead, use virtual environments or:
pip install --user scanpy
On MacOS, if not using
conda, you might need to install the C core of igraph via homebrew first
brew install igraph
If python-igraph still fails to install, see the question on compiling igraph. Alternatively consider installing gcc via
brew install gcc --without-multiliband exporting the required variables:
export CC="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X" export CXX="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"
xrefers to the version of
gcc; in my case, the path reads
On Windows, there also often problems installing compiled packages such as
but you can find precompiled packages on Christoph Gohlke’s unofficial binaries.
Download those and install them using
pip install ./path/to/file.whl
After downloading Miniconda, in a unix shell (Linux, Mac), run
cd DOWNLOAD_DIR chmod +x Miniconda3-latest-VERSION.sh ./Miniconda3-latest-VERSION.sh
and accept all suggestions.
Either reopen a new terminal or
source ~/.bashrc on Linux/
source ~/.bash_profile on Mac.
The whole process takes just a couple of minutes.