https://github.com/markziemann/5pillars
Five pillars of computational reproducibility
https://github.com/markziemann/5pillars
bioinformatics computational-biology data-science journal-article reproducible-research
Last synced: 5 months ago
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Five pillars of computational reproducibility
- Host: GitHub
- URL: https://github.com/markziemann/5pillars
- Owner: markziemann
- License: mit
- Created: 2023-05-26T01:10:03.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-02-06T23:49:19.000Z (over 2 years ago)
- Last Synced: 2024-05-09T21:13:42.183Z (about 2 years ago)
- Topics: bioinformatics, computational-biology, data-science, journal-article, reproducible-research
- Language: TeX
- Homepage: https://ziemann-lab.net/public/5pillars/5pillars.html
- Size: 721 KB
- Stars: 6
- Watchers: 3
- Forks: 2
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 5pillars
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:
* Code version control and persistent sharing.
* Compute environment control.
* Literate programming.
* Documentation.
* Persistent data sharing.
A live version of the manuscript is available at the Ziemann lab website [here](https://ziemann-lab.net/public/5pillars/5pillars.html).
## Contents
There are three folders:
* `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.
## Recipe
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
```
## How to contribute
Raise an issue on GitHub to report problems with the article or give your suggestions.
## Funding
No external funding was required.