README.md

Cytoscape Desktop in a Docker Image

Cytoscape Desktop in Docker image with GUI running using xvfb and VNC server

(Get the pre-built Docker image from dockerhub and) Run the image.

Launch Cytoscape with RStudio(+RCy3) in Docker

In a local terminal window, run the following command to create a Docker container for Cytoscape+R automation:

docker run -p 6080:6080 -p 8787:8787 cytoscape/cytoscape-desktop:rcy3-2.16.0

1. Open the URL below with your web browser:

• http://localhost:6080/vnc_auto.html
• http://localhost:8787/ (username: rstudio, password: cytoscape)

Launch Cytoscape with Jupyter(+py4cytoscape) in Docker

In a local terminal window, run the following command to create a Docker container for Cytoscape+Python automation:

docker run -p 6080:6080 -p 8888:8888 cytoscape/cytoscape-desktop:py4cytoscape-1.3.0

1. Open the URL below with your web browser:

• http://localhost:6080/vnc_auto.html
• http://localhost:8888/lab

Launch Cytoscape only in Docker

In a local terminal window, run the following command to create a Docker container for Cytoscape only:

docker run -p 6080:6080 cytoscape/cytoscape-desktop:3.9.1

1. Open the URL below with your web browser:

• http://localhost:6080/vnc_auto.html

(Or) Build the image yourself

Clone this repo, cd into it and build the image yourself

For Cytoscape Automation with RCy3

git clone https://github.com/cytoscape/docker-cytoscape-desktop
cd docker-cytoscape-desktop/rcy3
docker build -t cytoscape/cytoscape-desktop:rcy3-2.16.0 .

For Cytoscape Automation with py4cytoscape

git clone https://github.com/cytoscape/docker-cytoscape-desktop
cd docker-cytoscape-desktop/py4cytoscape
docker build -t cytoscape/cytoscape-desktop:py4cytoscape-1.3.0 .

Just for Cytoscape

git clone https://github.com/cytoscape/docker-cytoscape-desktop
cd docker-cytoscape-desktop/base
docker build -t cytoscape/cytoscape-desktop:3.9.1 .