Please note that this project has been superceded by the py4cytoscape project. py2cytoscape is not currently maintained.
py2cytoscape can be installed using conda, pip.
conda installs igraph with py2cytoscape.
You do not need to install igraph by yourself.
conda install -c conda-forge py2cytoscapepip3 install py2cytoscapepip3 install git+https://github.com/cytoscape/py2cytoscape.gitgit 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 ${LDFLAGS}"
export LDFLAGS
PKG_CONFIG_PATH=igraphcore/_install/lib/pkgconfig/
export PKG_CONFIG_PATH
python3 setup.py install --user
Package documentation can be found on https://py2cytoscape.readthedocs.io.
For contributing please check the wiki.
Full workflows can be found on the cytoscape/cytoscape-automation repo. The following workflows include cyrest usage:
Please do all your development in our development docker image:
docker pull mpgagebioinformatics/py2cytoscape:latest
- Create a folder to map to the container's user home folder
mkdir -p ~/py2cy-container
- Start the container from the latest version of the image
sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/py2cy-container:/home/mpiage --name py2cy-container \
-it mpgagebioinformatics/py2cytoscape:latest
- Alternatively you can start the container from a specific tag/version of the image
sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/py2cy-container:/home/mpiage --name py2cy-container \
-it mpgagebioinformatics/py2cytoscape:<tag>
- Connect to the running container
sudo docker exec -i -t py2cy-container /bin/bash
- Stop the container
sudo docker stop py2cy-container
- Jupyter
Once you have connected to the running container you can start jupyter with
module load jupyterhub
jupyter notebook --ip=0.0.0.0
A URL will be presented to you, and it should be pasted into your host's browser (Chrome recommended).
- RStudio-server
Once you have connected to the running container you can start
Rstudio serverwith
module load rlang
sudo rstudio-server start
You can then get access by connecting on your host's browser to http://localhost:8787.
For stopping the server use:
sudo rstudio-server stop
- X forward to enable Cytoscape
On a Mac install socat and xquartz:
brew install socat
brew install xquartz
Open Xquartz:
open -a Xquartz
Then navigate to XQuartz > Preferences > Security and tick the box 'Allow connections from network clients'.
Check your ip address:
IP=$(ifconfig en0 | grep inet | awk '{ print $2 }')
Start socat:
socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"
an then start the container by adding the -e DISPLAY=${IP}:0 argument.
Complete example call:
IP=$(ifconfig en0 | grep inet | awk '{ print $2 }') && \
socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\" & \
docker run -d -e DISPLAY=${IP}:0 -p 8787:8787 -p 8888:8888 \
-v ~/py2cy-container:/home/mpiage --name py2cy-container \
-it mpgagebioinformatics/py2cytoscape:latest
- User account
User: mpiage
Pass: bioinf
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.