cergare/microbiome-lesson

Carpentry-style lesson on microbiodata data analysis

Microbiota data analysis

This repository generates the microbiota data analysis lesson materials based on the website template from The Carpentries Foundation.

Preview changes to the lesson locally

The lesson website is built through Github and Jekyll.

Option 1: follow the Carpentries setup: http://carpentries.github.io/lesson-example/setup.html The detailed instructions are listed in the "Jekyll Setup for Lesson Development" section.

Option 2: use a Docker container

1. Open a Shell window.
2. Navigate to the microbiome-lesson/ folder using the cd command.
3. Since the lesson relies Jekyll 3.8.5, type within the Shell export JEKYLL_VERSION=3.8.5.
4. Make sure you have Docker for Windows or Mac installed: https://docs.docker.com/install/
5. With the Docker Desktop application running (you should see a little whale with containers at the top of your screen), type docker run --rm --volume="$PWD:/srv/jekyll" -p 4000:4000 -it jekyll/jekyll:$JEKYLL_VERSION jekyll serve
6. Open a web browser and type http://0.0.0.0:4000/ in the navigation bar. You should see the lesson website. Your changes should be automatically reflected online.

Maintainer(s)

Current maintainers of this lesson are

• Marc Galland, Data analyst and manager (University of Amsterdam, SILS, Plant Physiology Department).
• Anouk Zancarini, Assistant-Professor (University of Amsterdam, SILS, Plant Hormone Biology).

Authors

A list of contributors to the lesson can be found in AUTHORS

Citation

To cite this lesson, please consult with CITATION

Credits

Materials have been adapted and some exercises created to comply with the Carpentries Foundation teaching requirements.

Contributing

We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.

We'd like to ask you to familiarize yourself with our Contribution Guide and have a look at the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even how to write new episodes.

Please see the current list of [issues][FIXME] for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter Contributing to a Project in Pro Git by Scott Chacon. Look for the tag . This indicates that the mantainers will welcome a pull request fixing this issue.