Using Docker as a Personal Productivity Tool – Running Command Line Apps Bundled in Docker Containers

May 3, 2016

(This article was first published on Rstats – OUseful.Info, the blog…, and kindly contributed to R-bloggers)

With its focus on enterprise use, it’s probably with good reason that the Docker folk aren’t that interested in exploring the role that Docker may have to play as a technology that supports the execution of desktop applications, or at least, applications for desktop users. (The lack of significant love for Kitematic seems to be representative of that.)

But I think that’s a shame; because for educational and scientific/research applications, docker can be quite handy as a way of packaging software that ultimately presents itself using a browser based user interface delivered over http, as I’ve demonstrated previously in the context of Jupyter notebooks, OpenRefine, RStudio, R Shiny apps, linked applications and so on.

I’ve also shown how we can use Docker containers to package applications that offer machine services via an http endpoint, such as Apache Tika.

I think this latter use case shows how we can start to imagine things like a “digital humanities application shelf” in a digital library, that allows users to take either an image of the application off the shelf (where an image is a thing that lets you fire up a pristine instance of the application), or a running instance of the application of the shelf. (Furthermore, the application can be run locally, on your own desktop computer, or in the cloud, for example, using something like a mybinder like service). The user can then use the application directly (if it has a browser based UI), or call on it from elsewhere (eg in the case of Apache Tika). Once they’re done, they can keep a copy of whatever files they were working with and destroy their running version of the application. If they need the application again, they can just pull a new copy (of the latest version of the app, or the version they used previously) and fire up a new instance of it.

Another way of using Docker came to mind over the weekend when I saw a video demonstrating the use of the contentmine scientific literature analysis toolset. The contentmine installation instructions are a bit of a fiddle for the uninitiated, so I thought I’d try to pop them into a container. That was easy enough (for a certain definition of easy – it was a faff getting node to work and npm to be found, the Java requirements took a couple of goes, and I;m sure the image is way bigger than it really needs to be…), as the Dockerfile below/in the gist shows.

But the question then was how to access the tools? The tools themselves are commandline apps, so the first thing we want to do is to be able to call into the container to run the command. A handy post by Mike English entitled Distributing Command Line Tools with Docker shows how to do this, so that’s all good then…

The next step is to consider how to retain copies of the files created by the command line apps, or pass files to the apps for processing. If we have a target host directory and mount it into the container as as a shared volume, we can keep the files on our desktop or allow the container to create files into the host directory. Then they’ll be accessible to us all the time, even if we destroy the container.

The gist that should be embedded below shows the Dockerfile and a simple batch file passes the Contentmine tool commands into the container which then executes them. The batch file idea could be further extended to produce a set of command shortcuts that essentially alias the Contentmine commands (eg a ./getpapers command rather than a ./contentmine getpapers command, or that combine the various steps associated with a particular pipeline or workflow – getpapers/norma/cmine, for example – into a single command.

If there are other folk out there looking at using Docker specifically for self-managed “pull your own container” individual desktop/user applications, rather than as a devops solution for deploying services at scale, I’d love to chat…:-)

The rest of the way this post is published is something of an experiment – everything below the line is pulled in from a gist using the WordPress – embedding gists shortcode…

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