In this repo I’ve included an example project associated with a presentation initially given at R-Ladies Montpellier called ‘Gold star reproducibility: straightforward containerisation’. The presentation is included both as a keynote file (so you can enjoy the gifs) or as a pdf (static. sad face).
The example project is extremely simple, as it was only for illustration. I’ve written a meagre rmarkdown file (‘my_brilliant_paper’) that includes use of one package: ggplot2. The idea behind holepunch is that with a few simple functions you can set up your project so that it can be accessed in a container hosted on a server by binder. The readme for holepunch is a fantastic resource.
In the presentation, I demo’d this workflow with the following steps of code, that prepared this repo. First, you write a description file. Holepunch finds the packages you use without you having to troll through and specify them. We can see in ours that in addition to ggplot2 it has added rmarkdown, knitr, and tinytex, which are needed to knit ‘my_brilliant_paper’.
holepunch::write_compendium_description()I filled in my project name and description in the description file itself. Next, we use this description file to write up a docker file.
holepunch::write_dockerfile('Saras Windecker')A dockerfile is basically the set of instructions that are used to prepare an ‘image’, where these items are downloaded. This image can be launched to open up a ‘container’ inside which you have everything you specified in the dockerfile. This is a non-computer scientists’ take on this complicated process.
Lastly, we generate the link to our binder, so that we can advertise it and others can try and recreate our work inside a space that has everything downloaded that is necessary to rerun the project.
holepunch::generate_badge()This function prints the badge text to your console, that you can then paste into a readme file. Let’s take a look at ours now:
A complete example for a paper can be found here!
I will be revising this repo and its contents as I prepare to give this presentation in the future. Any comments are welcome. Happy containerising!