Adventures in replicable scientific papers: Docker

About a month ago, I took some time to try out Docker, a container technology that lets you bundle together, distribute, and execute applications in a lightweight Linux container. It seemed neat but I didn't apply it to any real problems. (Heng Li also tried it out, and came to some interesting conclusions -- note especially the packaging discussion in the comments.)

At the sprint, I decided to try building a software container for our latest paper submission on semi-streaming algorithms for DNA sequence analysis, but I got interrupted by other things. Part of the problem was that I had a tough time conceptualizing exactly what my use case for Docker was. There are a lot of people starting to use Docker in science, but so far only has really demonstrated its utility.

Fast forward to yesterday, when I talked with Michael Crusoe about various ideas. We settled on using Docker to bundle together the software needed to run the full paper pipeline for the streaming paper. The paper was already highly replicable because we had used my lab's standard approach to replication (first executed three years ago!) This wasn't a terribly ambitious use of Docker but seemed like it could be useful.

In the end, it turned out to be super easy! I installed Docker on an AWS m3.xlarge, create a Dockerfile, and wrote up some instructions.

The basic idea we implemented is this:

  • install all the software in a Docker container (only needs to be done once, of course);
  • clone the repository on the host machine;
  • copy the raw data into the pipeline/ sub-directory of the paper repository;
  • run the docker container with the root of the paper repository (on the host, wherever it might be) bound to a standard location ('/paper') in the image;
  • voila, raw data in, analyzed results out!

(The whole thing takes about 15 hours to run.)

The value proposition of Docker for data-intensive papers

So what are my conclusions?

I get the sense that this is not really the way people are thinking about using Docker in science. Most of what I've seen has to do with workflows, and I get the sense that the remaining people are trying to avoid issues with software packaging. In this case, it simply didn't make sense to me to break our workflow steps for this paper out into different Docker images, since our workflow only depends on a few pieces of software that all work together well. (I could have broken out one bit of software, the Quake/Jellyfish code, but that was really it.)

I'm not sure how to think about the volume binding, either - I'm binding a path on the Docker container directly to a local disk, so the container isn't self-sufficient. The alternative was to package the data in the container, but in this case, it's 15-20 GB, which seemed like too much! This dependence on external data does limit our ability to deploy the container to compute farms though, and it also means that we can't put the container on the Docker hub.

The main value that I see for this container is in not polluting my work environment on machines where I can run Docker. (Sadly this does not yet include our HPC at MSU.) I could also use a Project Jupyter container to build our figures, and perhaps use a separate Latex container to build the paper... overkill? :).

One nice outcome of the volume binding is that I can work on the Makefile and workflow outside of the docker container, run it all inside the container, and then examine the artifacts outside of the container. (Is there a more standard way to do this?)

I also really like the explicit documentation of the install and execution steps. That's super cool and probably the most important bit for paper replication. The scientific world would definitely be a better place if the computational setup for data analysis and modeling components of papers came in a Dockerfile-style format! "Here's the software you need, and the command to run; put the data here and push the 'go' button!"

I certainly see the value of docker for running many different software packages, like does. I think we should re-tool our k-mer counting benchmark paper to use containers to run each k-mer counting package benchmark. In fact, that may be my next demo, unless I get sidetracked by my job :).

Next steps

I'm really intrigued by two medium-term directions -- one is the bioboxes-style approach for connecting different Docker containers into a workflow, and the other is the approach for benchmarking software. If this benchmarking can be combined with github repos ("go benchmark the software in this github project!") then that might enable continuously running testing and benchmarks on a wide range of software.

Longer term, I'd like to have a virtual computing environment in which I can use my Project Jupyter notebook running in a Docker environment to quickly and easily spin up a data-intensive workflow involving N docker containers running on M machines with data flowing through them like so. I can already do this with AWS but it's a bit clunky; I foresee a much lighter-weight future for ultra-configurable computing.

In the shorter term, I'm hoping we can put some expectations in place for what dockerized paper replication pipelines might look like. (Hint: binary blobs should not be acceptable!) If we have big data sets, we probably don't want to put them on the Docker Hub; is the right solution to combine use of a data repository (e.g. figshare) with a docker container (to run all the software) and a tag in a github repository (for the paper pipeline/workflow)?

Now, off to review that paper that comes with a Docker container... :)


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