EBI-Metagenomics / holofood-course

ReadTheDocs/Sphinx documentation source for the "Organisation and utilisation of hologenomic datasets" Holofood course, 2022

Holofood Course: workshop notes

Organisation and utilisation of hologenomic datasets

This repository contains the source of the workshop notes of the "Organisation and utilisation of hologenomic datasets" course.

The notes are written using Sphinx/RST. It is a markup language.

The notes are built automatically to a ReadTheDocs site: https://holofood-course.rtfd.io

Using the course notes

Head to the live documentation page

Adding to the course notes (as a course instructor)

• Clone this repository.
• (Optional): create a virtualenv / conda env. Sphinx uses Python.
• pip install -r requirements.txt
• Run Sphinx in watch mode, to build and serve the notes website as you write:
  • sphinx-autobuild . _build/html --port 8000
  • Go to the locally served documentation site to see what your notes look like.
• Add a sub-directory for your course session to the sessions directory.
  • You can add .rst files and images etc as you wish. The Sphinx website has good tutorials for using .rst if you are new to it.
  • There is a stub example under session/metagenomics.
• Add a line to the index.rst table-of-contents with the path to your new .rst file(s).
• Open a pull request on GitHub to merge your changes in with everybody else's.

Where to store other course assets (as a course instructor)

• You can also add a few scripts or notebooks or small datafiles etc to this repository, if they're needed for your course session.
• For big (>20MB) datafiles, host them elsewhere e.g. on an FTP server. During the course itself, we have S3 available for this purpose.
• Use of Docker is fine / encouraged for packing software requirements. Quay.io is a good option for building/hosting these images.