Docker-Bioconductor-Cytoscape

Docker file for kristiyanto/networkbma.

The package contains: Cytoscape, R, with Bioconductor packages (igraph, Rserve, and networkBMA).

A tutorial to get it run on Windows and Mac are available: https://www.youtube.com/watch?v=FXOU2EZ4szI (Mac) https://www.youtube.com/watch?v=Y1Ye5mOMBW0 (Windows)

OSX

PREPARATION

Install Docker

https://www.docker.com/toolbox

Install Brew

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install X11 (XQuartz)

brew install xquartz

Install Socat

brew install socat

TO RUN CONTAINER

Get the Socat running

socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:"$DISPLAY"

Get XQuartz Running

open -a Xquartz

Get Docker Running

(Run Kitematic)

Run the Image (IP is your Mac IP, use ifconfig command if not sure)

docker run -ti -e DISPLAY=192.168.99.1:0 kristiyanto/networkbma

WINDOWS

PREPARATION

Install Docker

https://www.docker.com/toolbox

Install MobaXterm

http://mobaxterm.mobatek.net/

TO RUN CONTAINER

Get Docker running

(run kitematic)

Open MobaXterm with X11 Support

(tools -> X11 tab with DWM)

Login into Docker VM

ssh -X [email protected]

password is tcuser, ip is your docker VM IP. If not sure, run: docker-machine ip default

Run Docker

docker run -ti -e DISPLAY=192.168.99.1:1.0 kristiyanto/networkbma

IP is your Windows IP address. Use ipconfig if not sure. Display port (:1.0) is your current display port. Look at your MobaXterm window tab name if not sure.