pip3
to access Python 3):[leiden]
installs two packages that are needed for popularparts of scanpy but aren’t requirements: python-igraph[Csardi06] and leiden[Traag18].cd
intoits root directory. To install using symbolic links (stay up to date with yourcloned version after you update with gitpull
) call:Permissiondenied
error, never use sudopip
. Instead, use virtual environments or:conda
, you might need to install the C core of igraph via homebrew firstbrewinstalligraph
brewinstallgcc--without-multilib
and exporting the required variables:X
and x
refers to the version of gcc
;in my case, the path reads /usr/local/Cellar/gcc/6.3.0_1/bin/gcc-6
.igraph
,but you can find precompiled packages on Christoph Gohlke’s unofficial binaries.Download those and install them using pipinstall./path/to/file.whl
source~/.bashrc
on Linux/ source~/.bash_profile
on Mac.The whole process takes just a couple of minutes.