webdatascience / guidock

GUIdock: Using Docker containers with a common graphics user interface to address the reproducibility of research

GUIdock is a Docker Package containing the entire computational environment to run applications with a graphical user interface. As a proof of concept, we focus on supporting Cytoscape, a Java-based standalone program with a graphical user interface for the visualization and analyses of gene networks in biology. In addition to Cytoscape, our container includes R, Rserve, Bioconductor packages igraph, networkBMA and a Cytoscape app called CyNetworkBMA. GUIdock contains the entire pipeline and all the tools (including Cytoscape that connects to preloaded RServe, a Bioconductor package called “networkBMA” and all its dependencies) to generate gene regulatory networks.

Docker file for biodepot/GUIdock (Docker Hub Page)

Source code, installation and running script, and Dockerfile available at: https://github.com/BioDepot/GUIdock

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

Demonstration video (for Linux, Mac, and Windows)

Publication

Hung, Ling-Hong, Daniel Kristiyanto, Sung Bong Lee, and Ka Yee Yeung. "GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research." PloS one 11, no. 4 (2016): e0152686.

http://dx.doi.org/10.1371/journal.pone.0152686

Linux

Install and Run

Download and run runGUIdockLinux.sh from installation folder.
Usage:

sh runGUIdockLinux.sh

The script creates folder ~/.guidock/GUIdock-SHARED within user's home directory. The folder is linked to /root/GUIdock-SHARED in the container.

Instructional Video: https://www.youtube.com/watch?v=HOtI1Eg2J1Q

OSX

Install

Docker Toolbox needs to be downloaded and installed manually from the website. https://www.docker.com/toolbox

In addition to Docker Toolbox, GUIdock requires Socat and XQuartz. Download and run install-mac.sh from Installation folder.
Usage:

sh install-mac.sh

Run GUIdock

To Run GUIdock, download and run start-mac.sh from Installation folder.
Usage:

sh start-mac.sh

Instructional Video: https://www.youtube.com/watch?v=4Qg0fCDOxhY

WINDOWS

Install

Download and install Docker Toolbox from: https://www.docker.com/toolbox
Download and install MobaXterm from: http://mobaxterm.mobatek.net/

Run GUIdock

Download RunGUIdock.sh and startMoba.bat from Installation folder.
Execute RunGUIdock.sh by double-click or by running from Windows Powershell:

sh RunGUIdock.sh

Instructional Video: https://www.youtube.com/watch?v=cA7HVCB064I

Contact

Ling-Hong Hung, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung
Institute of Technology
University of Washington
Tacoma, WA 98402, USA

guidock's Issues

Issues with windows script

Hi,
I tried to run your script on Windows 7 (in GUIdock-Win.zip) and I had some issues :).
First was that I could not execute the bash script simply by double-clicking.
I tried executing the script from the mobaxterm terminal, but I had problems with line15 as mobaxterm uses a different directory structure (?)
I tried with cygwin then.
Line 20 caused a syntax_error that was fixed by changing //v to /v.
Also the way mobaxterm is started in line 64 does not allow whitespaces in the directory names. This shouldn't be much of a problem, but the way errors are handled makes it impossible to see this quickly (It just said : Looks like something went wrong... Press any key to continue...)
After this I got your examples to work really quickly. If I now want to run my own image I just have to change it in the script in line6 or is there something else that I have to take into account?

Please pull remotes/origin/GUIdock_novnc_dockerimage from varunmittal91/GUIDock

Hi Daniel,
Please pull the above mentioned branch, it has the trigger from docker hub to generate dockerimage automatically.