https://github.com/southgreenplatform/training_reproducible_research
Training on Tools for Reproducible Research given by SouthGreen
https://github.com/southgreenplatform/training_reproducible_research
conda container git notebook quarto rmarkdown snakemake
Last synced: 7 months ago
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Training on Tools for Reproducible Research given by SouthGreen
- Host: GitHub
- URL: https://github.com/southgreenplatform/training_reproducible_research
- Owner: SouthGreenPlatform
- License: cc-by-4.0
- Created: 2023-03-27T13:33:46.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-06-15T10:03:22.000Z (about 3 years ago)
- Last Synced: 2024-04-13T07:34:32.160Z (over 2 years ago)
- Topics: conda, container, git, notebook, quarto, rmarkdown, snakemake
- Language: Python
- Homepage: https://southgreenplatform.github.io/training_reproducible_research/
- Size: 57.8 MB
- Stars: 3
- Watchers: 6
- Forks: 3
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[![CC BY 4.0][cc-by-shield]][cc-by]
# Tools for Reproducible Research
---------------------------
## Table of Contents
* [Foreword](#foreword)
* [Project layout](#project-layout)
* [For collaborators teachers and developers](#for-collaborators-teachers-and-developers)
* [Modify content](#modify-content)
* [MkDocs](#mkdocs)
* [Welcome to MkDocs](#welcome-to-mkdocs)
* [Installation](#installation)
* [Manual](#manual)
* [Conda](#conda)
* [Testing and building the website](#testing-and-building-the-website)
* [Acknowledgement](#acknowledgement)
* [License](#license)
## Foreword
The course itself lives [https://southgreenplatform.github.io/training_reproducible_research/](https://southgreenplatform.github.io/training_reproducible_research/),
where you can find all the relevant information.
This work is based on the NBIS / ELIXIR *Tools for Reproducible Research* course.
## Project layout
```
README.md # General readme
mkdocs.yml # The configuration file for the site rendering.
conda_env.yml # Conda env to build and test the site locally
docs/ # material that will be publish with the static web site
index.md # The documentation homepage (Website Home page).
pages/ # Folder dedicated to the course materials use by mkdocs for the website
images # Images used in the course materials in general
xxx/ # Folder containning the course materials for one topic
xxx.md # Page taking about all or a part of the topic
images/ # Images related to the topic
...
lectures/ # Folder dedicated to lectures (within docs to ease embedding within the course)
README.md # readme
environment.yml # conda env to use for rendering the Rmarkdown lecture files
template.css # CSS used by all Rmarkdown lecture files
Snakefile # Automating rendering of all Rmarkdown lecture files
xxx # folder related to one lecture
xxx.Rmd # Lecture in Rmarkdown format
xxx.pdf # PDF rendering of Rmarkdown file
xxx.html # HTML rendering of Rmarkdown file
tutorials/ # Folder dedicated to tutorials
xxx # folder related to one tutorial
Images # Images used in the README
```
## For collaborators teachers and developers
This part is for collaborators-teachers and developers.
### Modify content
When you are in the repository, add and/or modify your markdown tutorials in the docs directory.
The arborescence of the website menu is to setup in the `mkdocs.yml` file
### Mkdocs
#### Welcome to MkDocs
For full documentation visit [mkdocs.org](https://www.mkdocs.org).
For full documentation about the [material mkdocs theme](https://squidfunk.github.io/mkdocs-material/).
#### Installation
##### Manual
As prerequisite you need python >=3.8 and pip.
Install Mkdocs:
`pip install mkdocs`
For the theme:
`pip install mkdocs-material`
For the extensions:
`pip install pymdown-extensions`
For the plugins:
`pip install mkdocs-minify-plugin`
`pip install mkdocs-macros-plugin`
`pip install mkdocs-embed-external-markdown`
##### Conda
Clone the repository and move in it.
Then install all dependencies using conda and the `conda_env.yml` shipped with this repo:
```
conda env create -f conda_env.yml
```
Activate the environment and you are good:
```
conda activate education
```
#### Testing and building the website
* `mkdocs serve` - Start the live-reloading docs server, to test the site locally (http://127.0.0.1:8000/).
* `mkdocs gh-deploy` - Deploys the site on github pages.
* `mkdocs build` - Build the documentation site.
* `mkdocs new [dir-name]` - Create a new project.
* `mkdocs -h` - Print help message and exit.
## Acknowledgement
* NBIS - This work is based on the NBIS / ELIXIR course *Tools for Reproducible Research* that can be found [here](https://github.com/NBISweden/workshop-reproducible-research).
[
](https://nbis.se)
* @jhayer and @HadrienG about help in use and rendering with mkdocs and other features.
* All contributors
## License
This work is licensed under a [Creative Commons Attribution 4.0 International License][cc-by].
[cc-by]: http://creativecommons.org/licenses/by/4.0/
[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg