py2cytoscape

Installation

py2cytoscape can be installed using conda, pip.

conda

conda installs igraph with py2cytoscape. You do not need to install igraph by yourself.

conda install -c conda-forge py2cytoscape

Latest stable release (pip)

pip3 install py2cytoscape

Development version (pip)

pip3 install git+https://github.com/cytoscape/py2cytoscape.git

Dependencies (extra): igraph

git clone https://github.com/igraph/python-igraph/
cd python-igraph

git clone https://github.com/igraph/igraph igraphcore
cd igraphcore
./bootstrap.sh
mkdir _build && cd _build
../configure --prefix=$PWD/../_install
make
make install
cd ../../

CPPFLAGS="-I$PWD/igraphcore/_install/include/igraph ${CPPFLAGS}"
export CPPFLAGS
LDFLAGS="-L$PWD/igraphcore/_install/lib ${LDFLAGS}"
export LDFLAGS
PKG_CONFIG_PATH=igraphcore/_install/lib/pkgconfig/
export PKG_CONFIG_PATH

python3 setup.py install --user

Documentation

Package documentation can be found on https://py2cytoscape.readthedocs.io.

For contributing please check the wiki.

Full workflows can be found on the cytoscape/cytoscape-automation repo. The following workflows include cyrest usage:

advanced-cancer-networks-and-data

Citing

Ono, K. et al. (2015) CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res, 4, 478

Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.

satyakam001/py2cytoscape