Introduction to containers and Snakemake course website

• 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 👍. Please have a look at the CONTRIBUTING.md file to learn more on how to contribute.

Authors

• Antonin Thiébaut ORCiD
• Geert van Geest ORCiD
• Patricia Palagi ORCiD

How to reuse this material?

This is a combination of the introduction to containers course with a module on Snakemake. The markdown files of the container course are added as a module.

To clone the entire repository:

• Clone the repository:

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

• Initialise the submodules:

   cd containers-snakemake-training
   git submodule update --init --recursive
   git submodule update

• Update to the most recent version of the submodules:

   git submodule update --remote

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 MkDocs, with the Material theme.

• Install MkDocs:

   pip install mkdocs

• And Material:

   pip install mkdocs-material

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

   mkdocs serve

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

How to generate a github page?

For an automatically generated github page, you can run:

mkdocs gh-deploy