Docker image for Foroutan et al. paper

This repository contains instructions to run Docker images that reproduce the figures and results for the following paper:

A Transcriptional Signature for TGFβ-induced EMT in Cancer

Momeneh Foroutan, Joseph Cursons, Soroor Hediyeh-Zadeh, Erik W. Thompson and Melissa J. Davis

Download Instructions

Two separate images have been prepared that reproduce the cell-line analysis and the tumour analysis.

Download and install Docker.

To reproduce the results for the cell-line analysis

Start Docker and run the following command:

docker run -p 49000:8787 -d davislaboratory/mforoutan_tgfb_2017_celllines

(You can replace 49000 with another open port if you want.) Navigate in your web browser to http://0.0.0.0:49000. This will open up rstudio. The username and password are both davislab. You can run generate_all_experiments.R to reproduce all the figures and results from Foroutan et al.

# In rstudio run: 
source("generate_all_experiments.R")

To reproduce the results for the tumours analysis

Run the following command:

docker run -p 49000:8787 -d davislaboratory/mforoutan_tgfb_2017_tumours

then follow the above instructions. Please make sure you have stopped the running image/containers before running the other image, when running an image through the same port. Alternatively, the images can be run through different ports. Running containers/image can be stopped using the following command:

docker stop $(docker ps -aq)

Note: If the error 'port is allocated' is encountered, please try to stop the running image using above instructions.

Running on a Mac

If you are running on a Mac, you should have already installed either Docker for Mac, or Docker Toolbox. Instructions are the same as above if you're using Docker for Mac. However, if you're using Docker Toolbox you would need to replace "0.0.0.0" with your IP address. You're IP address is displayed once you run the Docker Quick Terminal from Docker Toolbox.Then navigate in the browser to $IP:49000.

Please note that some of the scripts provided with the image perform computationally intensive operations. Our testings suggest that Mac users running Docker Toolbox will have difficulties running some of the scripts due to CPU limitations of Virtualbox-based Docker machines. Users are, therefore, strongly encouraged to install and run Docker for Mac.

Please contact Soroor ([email protected]) for bug reports or help requests, or simply open an issue.