flockowak/cytoscape repository overview

⁠What's in this image?

⁠Version 3.6.1 (latest)

• RStudio Server 3.5.0 from rocker⁠/rstudio⁠
• Cytoscape 3.6.1 from http://chianti.ucsd.edu/cytoscape-3.6.1/Cytoscape_3_6_1_unix.sh⁠
• Cytoscape and NDEx script from https://github.com/cytoscape/RCy3/raw/master/vignettes/Cytoscape-and-NDEx.Rmd⁠

⁠Version 3.6.0

• RStudio Server 3.4.1 from rocker⁠/rstudio⁠

• Cytoscape 3.6.0 (pre-release) from http://code.cytoscape.org/jenkins/job/cytoscape-3-gui-distribution/3595/org.cytoscape.distribution$cytoscape/artifact/org.cytoscape.distribution/cytoscape/3.6.0-20171018.011314-1020/cytoscape-3.6.0-20171018.011314-1020.tar.gz⁠ (18.10.2017 01:03:58)

  Also the following scripts from the Cytoscape Github⁠ are downloaded and can be found at /home/rstudio

  • check-library-installation.R
  • check-cytoscape-connection.R

⁠Exposed Ports

• 8787 used by RStudio
• 1234 used by CyREST (Swagger API)

⁠Usage

⁠Run container

docker run -dit \
	-p 8787:8787 \
	-p 1234:1234 \
	-v /tmp/.X11-unix:/tmp/.X11-unix \
    -e DISPLAY=$DISPLAY \
	--name=cytoscape-rstudio \
	flockowak/cytoscape

By default the username/password is rstudio:rstudio. To use a custom password by specifying the PASSWORD environmental variable

docker run -dit \
	-p 8787:8787 \
	-p 1234:1234 \
	-v /tmp/.X11-unix:/tmp/.X11-unix \
    -e DISPLAY=$DISPLAY \
    -e PASSWORD=yourpasswordhere \
	--name=cytoscape-rstudio \
	flockowak/cytoscape

For more options see the documentation on the rocker/rstudio⁠ docker hub page.

⁠Note:

You have to authorize your user to access the X Server from another host using xhost:

xhost +si:localuser:$USER

or

xhost +local

⁠Start RStudio

Open http://localhost:8787⁠ in you browser

⁠Run Cytoscape

docker exec -u rstudio cytoscape-rstudio cytoscape

⁠Test installation

⁠Version 3.6.1

1. Start Cytoscape
2. Start RStudio
3. Run the provided script (or just parts): "Cytoscape-and-NDEx.Rmd" ...This will do the following: ...* Install the required libraries RCy3⁠ and ndexr⁠ ...* Download some networks from NDEx⁠ ...* Import a network from NDEx⁠ in Cytoscape ...* Send a network from RStudio to Cytoscape

For more examples, explore the RCy3 documentation

?RCy3

or have a look at Cytoscape-Tutorials⁠ or Cytoscape Advanced Topic: Automation⁠

⁠Version 3.6.0

To check, if all required libraries are installed, you can run the check-library-installation.R script in RStudio:

source('/home/rstudio/check-library-installation.R')

With Cytoscape running, you can test the connection between RStudio and Cytoscape running the check-cytoscape-connection.R script:

source('~/check-cytoscape-connection.R')

⁠See also:

• RStudio https://www.rstudio.com/⁠
• RStudio Docker Image https://hub.docker.com/r/rocker/rstudio/⁠
• Cytoscape http://www.cytoscape.org/⁠
• Cytoscape Tutorials https://cytoscape.github.io/cytoscape-tutorials⁠
• Cytoscape Tutorials on Github https://github.com/cytoscape/cytoscape-tutorials⁠
• RCy3 on Bioconductor https://www.bioconductor.org/packages/release/bioc/html/RCy3.html⁠
• RCy3 on GitHub https://github.com/cytoscape/RCy3⁠
• ndexr on Bioconductor https://bioconductor.org/packages/ndexr/⁠
• ndexr on GitHub https://github.com/frankkramer-lab/ndexr⁠
• Cytoscape Automation R Scripts on Github https://github.com/cytoscape/cytoscape-automation/tree/master/for-scripters/R⁠