maxibor / intro-to-ancient-metagenomics-book

Introduction to Ancient Metagenomics Book

Introduction to Ancient Metagenomics Book

This is the source material for the Introduction to Ancient Metagenomics text book developed for the SPAAM Summer School: Introduction to Ancient Metagenomics.

Development notes

This text book has been developed as a Quarto Book, allowing for both website and PDF formats.

I highly recommend installing VS Code (or your preferred text editor/IDE) and the corresponding Quarto extension for development. This allows rendering prior to pushing to GitHub, and debugging of any issues of the website view.

Locally

If adding a new section chapter:

1. Clone this repository or open on https://gitpod.io ¹

2. Make a new branch e.g. git switch -c new-chapter

3. Make a new .qmd file in the root directory

4. Images for the chapter should go into assets/images/chapters/

   • Do not place in docs/assets/images/chapters/!

5. Add the .qmd file to the _quarto.yml config file in the chapters: scope

6. Render the book the extensions' Quarto: Render Book command, or run the following

   quarto preview intro-to-ancient-metagenomics-book --render all --no-browser --no-watch-inputs   

7. Commit, push to GitHub, and open a PR against the master branch ²

General tips:

• Use the native markdown syntax for images (![](assets/images/chapters/<your_image>.png))
• For note blocks see the Quarto docs

Notes

Footnotes

1. I recommend installing the gitpod chrome extension which adds a nice shortcut button to the github repository next to the green 'code' button. ↩

2. If you're using gitpod and have a 'don't have permissions' error when pushing you may need to do the following: (1) Go to: https://gitpod.io/user/integrations (2) Press triple dots next to the GitHub Git Provider (3) Edit permissions so all permissions are ticked except for read:user ↩