DaMBi HPC Guide

Documentation site on Basic and Advanced usage of High-Performance Computing in Bioinformatics, hosted at https://saeyslab.github.io/dambi-hpc-guide/.

Usage

Building the book

If you'd like to develop and/or build the DaMBi HPC Guide book, you should:

Clone this repository
Run pip install -r requirements.txt (it is recommended you do this within a virtual environment)
(Optional) Edit the books source files located in the dambi_hpc_guide/ directory
Run jupyter-book clean dambi_hpc_guide/ to remove any existing builds
Run jupyter-book build dambi_hpc_guide/

A fully-rendered HTML version of the book will be built in dambi_hpc_guide/_build/html/.

To automatically build on changes during development, you can alternatively run an auto-reload server at http://127.0.0.1:8000 using the following command:

sphinx-autobuild dambi_hpc_guide dambi_hpc_guide/_build/html -b html

You can also set up a reproducible development in VS code using the Dev Containers functionality. After the dev container is set up the sphinx-autobuild command serves the book on localhost port 8000.

The book can also be built using Docker.

Build the Docker image with docker build -t dambihpcguide .
Build the book with docker run --rm -v /path/to/save/book:/book/dambi_hpc_guide/_build dambihpcguide

Hosting the book

Please see the Jupyter Book documentation to discover options for deploying a book online using services such as GitHub, GitLab, or Netlify.

For GitHub and GitLab deployment specifically, the cookiecutter-jupyter-book includes templates for, and information about, optional continuous integration (CI) workflow files to help easily and automatically deploy books online with GitHub or GitLab. For example, if you chose github for the include_ci cookiecutter option, your book template was created with a GitHub actions workflow file that, once pushed to GitHub, automatically renders and pushes your book to the gh-pages branch of your repo and hosts it on GitHub Pages when a push or pull request is made to the main branch.

Contributors

We welcome and recognize all contributions. You can see a list of current contributors in the contributors tab.

Credits