Installation¶
Anaconda¶
If you do not have a working installation of Python 3.6 (or later), consider installing Miniconda (see Installing Miniconda). Then run:
conda install seaborn scikit-learn statsmodels numba pytables
conda install -c conda-forge python-igraph leidenalg
Pull Scanpy from PyPI (consider using pip3
to access Python 3):
pip install scanpy
PyPI only¶
If you prefer to exclusively use PyPI run:
pip install 'scanpy[leiden]'
The extra [leiden]
installs two packages that are needed for popular
parts of scanpy but aren’t requirements: python-igraph [Csardi06] and leiden [Traag18].
Development Version¶
To work with the latest version on GitHub: clone the repository and cd
into
its root directory. To install using symbolic links (stay up to date with your
cloned version after you update with git pull
) call:
pip install -e .
If you intend to do development work, there are some extra dependencies you’ll want.
These can be install with scanpy
via:
pip install -e ".[dev,doc,test]"
Docker¶
If you’re using Docker, you can use the minimal fastgenomics/scanpy image from the Docker Hub.
Troubleshooting¶
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-multilib
and 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"
where
X
andx
refers to the version ofgcc
; in my case, the path reads/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-6
.
On Windows, there also often problems installing compiled packages such as igraph
,
but you can find precompiled packages on Christoph Gohlke’s unofficial binaries.
Download those and install them using pip install ./path/to/file.whl
Installing Miniconda¶
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.