kozo2/dockercytoscapedesktop repository overview

⁠Cytoscape Desktop in a Docker Image

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

This Docker image is built on top of the ubuntu:20.04 image.

https://hub.docker.com/_/ubuntu⁠

Cytoscape content at DockerHub can be found here:

https://hub.docker.com/u/cytoscape⁠

⁠Pull or Build

You have the option of pulling the latest container from DockerHub,

docker pull cytoscape/cytoscape-desktop:latest

or you can clone this repo, cd into it and build the container yourself

docker build -t cytoscape/cytoscape-desktop .

⁠Run

⁠Launch Cytoscape in Docker

In a local terminal window, issue the following commands to run this docker container and launch Cytoscape:

docker run -v /Users/user/dockerroot:/root -p 1234:1234 -p 5900:5900 cytoscape/cytoscape-desktop:latest

Note: Files saved in '/root' is accessible on the host system at '/Users/user/dockerroot'. For example, in R using the RCy3 package you will want to prepend this output path to all your save and export args:

output.path <- '/root/'
saveSession(paste0(output.path, 'my-session-file'))

Pro-tip: Before shutting down the container, be sure to check that all your output files have indeed been saved locally.

⁠Interact

⁠Local Shell

docker exec -it cy bash

⁠VNC

⁠RealVNC

Connect with VNC (https://www.realvnc.com/download/viewer/⁠) using the URL below:

• URL: localhost:5900

No password is required.

Additionally, the VNC viewer is available as a Chrome extension:

https://chrome.google.com/webstore/detail/vnc%C2%AE-viewer-for-google-ch/iabmpiboiopbgfabjmgeedhcmjenhbla?hl=en⁠

and accessible via this link in Chrome:

chrome://apps/

⁠TightVNC

Use TightVNC if having problems with right click on MacOS with noVNC and RealVNC: https://www.tightvnc.com/download.php⁠

Running Java-Based TightVNC Client

java VncViewer HOST localhost PORT 5900

⁠Stop

docker stop cy