ELIXIR Toolkit Theme

The ELIXIR toolkit theme is a Jekyll theme designed to support easy deployment of documentation websites but also more complex ones that require a central tool table and linking towards ELIXIR resources.

Its key features:

• Easy deployment using GitHub Pages or GitHub Actions
• Advanced content search
• Create your own look with the many theme variables and support for custom classes
• Support for a central tools table
• Integrated attribution for contributors, editors and supporting organizations
• Page tagging and listing of those tagged pages
• Linking to ELIXIR resources including Bio.tools, FAIRsharing, FAIR Cookbook, RDMkit, TeSS and DSW
• Easy side navigation, top navigation and footer management
• Mobile friendly
• Create website sections with each section having its own sidebar
• Out of the box search engine optimizations including schema.org attributes and many other metadata attributes
• Web analytics through Matomo, Google Analytics or Plausible

Enabling the theme on your Jekyll project

Use the theme as a remote theme and lock it to a released version in your _config.yml file:

remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@6.1.0

An exact version is recommended so a website rebuild cannot silently pull a different theme. Before starting or upgrading, read the release notes and use the Gemfile from the matching release tag. See Versions and upgrades for the complete workflow.

Using Ruby Gems (alternative)

Alternatively you can use the Ruby Gem of the theme (needed when using GitLab) by adding an exact version to your Jekyll site’s Gemfile:

gem "elixir-toolkit-theme", "6.1.0"

And add this line to your Jekyll site’s _config.yml:

theme: elixir-toolkit-theme

Deployment

Via GitHub Actions

1. Make sure you have a GitHub workflow file setup similar to the one in this repo at .github/workflows/jekyll.yml.
2. Go to Settings > Actions and enable Allow all actions and reusable workflows
3. Got to the Actions tab of the repository and trust the workflows to run.
4. Go to Settings > Pages and enable GitHub Actions as a source
5. Go to Environments > github-pages and remove the rule under Deployment branches if you want to deploy other branches than master or main via Workflow Dispatch (manually triggered action)
6. Trigger the workflow by pushing a change to main or manually trigger the actions within the Actions tab of the repository.

Via GitHub Pages

This is the quickest way to deploy the elixir-toolkit-theme, but gives less flexibility and does not allow you to make use of the new way of tagging tools. Visit the GitHub documentation to find out more about how to setup GitHub pages.

NOTE: This way of deploying does not support the tool-tag in the text of the markdown file to tag tools and resources.

Via GitLab Pages

Add an extra .gitlab-ci.yml file in the root of the repo with:

image: ruby:3.3

variables:
  JEKYLL_ENV: production

before_script:
  - bundle install

pages:
  stage: deploy
  script:
  - bundle exec jekyll build -d public
  artifacts:
    paths:
    - public
  only:
  - master

Locally using Jekyll

1. If not already present on your machine, install ruby.

2. Install Jekyll

   If you have never installed or run a Jekyll site locally on your computer, follow these instructions to install Jekyll: https://jekyllrb.com/docs/installation/

    gem install jekyll
   

3. Install dependencies

    bundle install
   

4. Deploy website locally in development mode:

    bundle exec jekyll serve
   

   If you want to deploy the website locally in production mode, do:

    JEKYLL_ENV=production PAGES_REPO_NWO='USER_OR_ORGANISATION/REPO_NAME' bundle exec jekyll serve --baseurl ""
   

   Where USER_OR_ORGANISATION/REPO_NAME is the GitHub USER_OR_ORGANISATION/REPO_NAME (to be found in the url).

5. To preview your site, in your web browser, navigate to http://localhost:4000.

Additional information can be found at the following link: https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll

Locally using Docker

If not already installed on your machine, install Docker. From the root of the elixir-toolkit-theme directory, run:

docker run -it --rm -p [::1]:4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && bundle install && bundle exec jekyll serve --host 0.0.0.0"

This will start the docker container and serve the website locally. Make sure the .\_site is not yet created to avoid permission errors.

This theme is known to be used in

• RDMkit (CONVERGE)
• WorkflowHub (EOSC-life project)
• RO-crate (EOSC)
• GPG RO-Crate Profile (University of Auckland eResearch)
• Infectious Diseases Toolkit (BY-COVID)
• FAIRDOM (FAIRDOM community)
• How-to-Guides (Australian BioCommons)
• Australian Tree of Life documentation (Australian BioCommons)
• SPLASH (ELIXIR Training platform)
• 1+MG Framework (GDI)
• Human ‘Omics Data Sharing Field Guide (Australian BioCommons)
• ERIM RDM Toolbox (ERIM NL)
• ABLeS (Australian BioCommons)
• TRE-FX (DARE UK, HDR UK)
• Norwegian Life Science RDM LookUp (ELIXIR Norway)
• RSQkit: Research Software Quality kit (EOSC-EVERSE)
• research-data.no (ELIXIR Norway & BOTT universities Norway)
• Learning-Library (Australian BioCommons)
• ELIXIR-IT Training Platform (ELIXIR IT)
• FAIRDOM-SEEK Documentation (SEEK community)
• FAIR Lesson Plan Handbook (ELIXIR Training platform)
• Data Steward Handbook (ELIXIR RDM Community)
• Fed-A-Crate (ELIXIR Fed-A-Crate project)
• Federated Learning toolkit (FLkit) (UHasselt)
• mTeSS-X (OSCARS project)
• Galaxy Codex (Galaxy Community)
• ELIXIR Software Management Plan (ELIXIR SMP Community)
• FAIR Metroline (Health-RI)
• Globus Community Australasia (AARNet)
• ELIXIR Research Software Ecosystem (RSEc) (ELIXIR Tools Platform)
• Knowledge Hub (Luxembourg National Data Service (LNDS))
• ELIXIR-ELITMa (ELIXIR Training platform)
• ELIXIR-GOBLET Train-the-Trainer (ELIXIR Training platform)
• Want your instance here? Open an issue

Dependencies

This theme would not be possible without following open source projects:

• Bootstrap5 - As main CSS framework
• DataTables - To generate tables that are sortable, searchable and contain pagination
• AnchorJS - Adds deep anchor links to the headings
• lunr.js - Main tool behind the search bar enabling content search
• jQuery - A fast, small, and feature-rich JavaScript library for easy scripting
• jekyll-table-of-contents - Lightweight JS script to render the table of contents
• Lucide - The main icon library used by the theme through its static icon font
• Font-Awesome - Icon library kept available for backwards compatibility, brand icons and markdown/sidebar content
• flag-icons - A curated collection of all country flags in SVG + css integration
• clipboard.js - Modern copy to clipboard. No Flash. Just 3kb gzipped clipboard.

Attribution

If you like our work, you can add following badge to the readme of your project:

[![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)

License

The theme source code is available as open source under the terms of the MIT License.

Bundled third-party libraries and assets retain their upstream licenses. In particular:

• Lucide static icon font assets are distributed under the ISC License. Some Lucide icons are derived from Feather and are covered by MIT as noted in the Lucide license file.
• Font Awesome Free assets use component-specific licenses: webfont files are under SIL OFL 1.1, CSS/code is under MIT, and SVG/JS icon assets are under CC BY 4.0. Brand icons are trademarks of their respective owners and should only be used to represent those brands.