py2cytoscape
DEPRECATION
Please note that this project has been superceded by the py4cytoscape project. py2cytoscape is not currently maintained.
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 ${LDFLAGS}"
export LDFLAGS
PKG_CONFIG_PATH=igraphcore/_install/lib/pkgconfig/
export PKG_CONFIG_PATH
python3 setup.py install --user
Documentation
Package documentation can be found on https://py2cytoscape.readthedocs.io.
For contributing please check the wiki.
Full workflows can be found on the cytoscape/cytoscape-automation repo. The following workflows include cyrest usage:
Contributing
Please do all your development in our development docker image:
docker pull mpgagebioinformatics/py2cytoscape:latest
- Create a folder to map to the container's user home folder
mkdir -p ~/py2cy-container
- Start the container from the latest version of the image
sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/py2cy-container:/home/mpiage --name py2cy-container \
-it mpgagebioinformatics/py2cytoscape:latest
- Alternatively you can start the container from a specific tag/version of the image
sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/py2cy-container:/home/mpiage --name py2cy-container \
-it mpgagebioinformatics/py2cytoscape:<tag>
- Connect to the running container
sudo docker exec -i -t py2cy-container /bin/bash
- Stop the container
sudo docker stop py2cy-container
- Jupyter
Once you have connected to the running container you can start jupyter
with
module load jupyterhub
jupyter notebook --ip=0.0.0.0
A URL will be presented to you, and it should be pasted into your host's browser (Chrome recommended).
- RStudio-server
Once you have connected to the running container you can start
Rstudio server
with
module load rlang
sudo rstudio-server start
You can then get access by connecting on your host's browser to http://localhost:8787.
For stopping the server use:
sudo rstudio-server stop
- X forward to enable Cytoscape
On a Mac install socat
and xquartz
:
brew install socat
brew install xquartz
Open Xquartz:
open -a Xquartz
Then navigate to XQuartz > Preferences > Security and tick the box 'Allow connections from network clients'.
Check your ip address:
IP=$(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
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.