This repo contains the manuscript entitled Five pillars of computational reproducibility. This is an effort to solidify some previously proposed best-practices into a simple infographic. It highlights the importance of these five concepts to reproducibility:
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Code version control and persistent sharing.
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Compute environment control.
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Literate programming.
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Documentation.
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Persistent data sharing.
A live version of the manuscript is available at the Ziemann lab website here.
There are three folders:
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manuscript: the source document and bibliography. -
img: images. -
LICENCE: MIT Licence. -
README.md: This helpful document. -
main.sh: Master script. Execute this to reproduce the manuscript HTML. Requries Docker. -
helper.sh: This is a helper script required by the main.sh script.
This is an executable manuscript, follow the recipe to reproduce it on your system.
REQUIREMENTS: Ubuntu 22 (or similar Unix system) with 1 CPU thread and 4GB RAM. Docker must be installed. To install it on Ubuntu, run the following in a terminal:
sudo apt update && sudo apt install docker.io #skip this if you have docker already installed
To generate the manuscript run the following in a terminal. It will take 2-3 minutes.
bash main.sh
If the process completed, the HTML document was copied from the container to the host. It can be visualised with firefox or your favourite web browser.
firefox 5pillars.html
Raise an issue on GitHub to report problems with the article or give your suggestions.
No external funding was required.