Installation¶
Anaconda¶
If you do not have a working Python 3.5 or 3.6 installation, consider installing Miniconda (see Installing Miniconda). Then run:
conda install seaborn scikit-learn statsmodels numba pytables
conda install -c conda-forge python-igraph louvain
Pull Scanpy from PyPI (consider
using pip3
to access Python 3):
pip install scanpy
PyPI only¶
If you prefer to exlcusively use PyPI run:
pip install scanpy[louvain]
or:
pip install scanpy python-igraph louvain
The extra [louvain]
installs two packages that are needed for
parts of scanpy but aren’t requirements: python-igraph [Csardi06] and louvain [Traag17].
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 .
Docker¶
If you’re using Docker, you can use the minimal fastgenomics/scanpy image from the Docker Hub.
Trouble shooting¶
If you do not have sudo rights (you get a Permission denied
error):
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 here or consider installing gcc via
brew install gcc --without-multilib
and exportingexport CC="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"; export CXX="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"
, whereX
andx
refers to the version ofgcc
; in my case, the path reads/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-6
.
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.