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Example of providing a docker container for reproducible analyses. This repository is intended to show how Docker can be used to easily reproduce figures, results, etc. from computational publications. The R scripts and data examples are taken or modified from [Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture]
( (see below) and are not my original work.

Running the docker

docker run -p 49000:8787 -d mgymrek/docker-reproducibility-example

(You can replace 49000 with another open port if you want.) Navigate in your web browser to This will open up rstudio. The username and password are both "guest". You can open files in the scripts/ directory and run them to reproduce figures S7B and S1 from Martin et al.

Running on a Mac

If you are running on a Mac, you should have already installed, initialized, and started boot2docker using the instructions here. Instructions are the same as above, except instead of using "" as the IP address, run:

boot2docker ip

to get the IP, then navigate in the browser to $IP:49000.


Note: posted R code is a modified version of the code posted by the authors of Martin et al: [Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture]
( Original code can be found here. Code is posted with submission from the original authors. Data files were copied from their site.


  • You might get an rstudio error "Error in : figure margins too large" if the plot area is too small (e.g. if you're using a small screen or if you squished the plot area to be smaller). In that case, enlarge the plot area and run again.
  • All the data required was provided in this docker. Ideally the data would be separate from the code in either another data container or mounted to a directory when you run docker. I didn't do that here because this issue doesn't allow mounting whole directories on OSX. If that is fixed I might update this.
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