Reproducible and Scalable Research with Snakemake and Software Containers

• Website is hosted at https://sib-swiss.github.io/containers-snakemake-training/latest/

• Please refer to issues for improvements/bugs for course material or the website

• Any contribution to this course material is highly appreciated :+1:. Please have a look at the CONTRIBUTING.md file to learn more on how to contribute

Authors

• Antonin Thiébaut ORCiD
• Rafael Riudavets Puig ORCiD
• Geert van Geest ORCiD
• Patricia Palagi ORCiD

How to host the website locally?

Once you have cloned the repo, you can host it on your local browser. The website is generated with Zensical, a modern static site generator built on the Material for MkDocs theme, and configured entirely through the existing mkdocs.yml (Zensical reads it natively, no config changes required).

• Clone the repository:

  git clone https://github.com/sib-swiss/containers-snakemake-training.git
  

• Create and activate a virtual environment (recommended):

  python3 -m venv .venv
  source .venv/bin/activate
  

• Install Zensical:

  pip install zensical
  

• Make sure you are in the repository directory and type:

  zensical serve
  

The website will be hosted on your local browser at http://localhost:8000/.

Note: Zensical is under active development. Plugin support is currently a subset of the MkDocs plugin ecosystem, with full parity planned for upcoming releases. If you rely on custom plugins in mkdocs.yml, check Zensical's compatibility notes before switching.

How to generate a github page?

Zensical does not ship a gh-deploy shortcut like MkDocs did. Instead, see Zensical's publishing guide for a ready-to-use GitHub Actions workflow that builds the site with zensical build --clean and deploys it to GitHub Pages on every push.

This repository publishes multiple versions of the course material (e.g. latest/, 2023.10/), which requires a versioning tool on top of the base publishing setup. Zensical integrates with a fork of mike (the versioning tool originally built for MkDocs) as a bridge solution until native versioning support lands. To publish a new version:

mike deploy --push --update-aliases <version> latest
mike set-default --push latest

Note that mike's Zensical fork isn't on PyPI yet — it must be installed directly from GitHub:

pip install git+https://github.com/squidfunk/mike.git