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
- Advanced content search
- Create your own look with the many theme variables
- Change style using custom classes
- Support for a central tools table
- Page tagging and listing of those tagged pages
- Linking to ELIXIR resources including Bio.tools, FAIRsharing, FAIR Cookbook, 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 matadata attributes
- Support for Google Analytics and Plausible
The quickest way to use the elixir-toolkit-theme is to use the GitHub pages remote theme feature in your config.yml file:
remote_theme: ELIXIR-Belgium/elixir-toolkit-themeIt also allows you to use a specific version of the theme by add @X.X.X to make sure your website keeps working iif breaking changes get introduced.
Alternatively you can install it as a Ruby Gem (preferred way if you use GitLab).
Add this line to your Jekyll site's Gemfile:
gem "elixir-toolkit-theme"And add this line to your Jekyll site's _config.yml:
theme: elixir-toolkit-themeView the documentation for usage information (under development).
This theme can be used to deploy the website using GitHub pages. Visit the GitHub documentation to find out more about how to setup GitHub pages.
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If not already present on your machine, install ruby. Note that incompatibility issues may arise with ruby 3.0.0 (released 25.12.20) or newer versions.
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Install Jekyll If you have never installed or run a Jekyll site locally on your computer, follow these instructions to install Jekyll:
- Install Jekyll on MacOS/Ubuntu/Other_Linux/Windows: https://jekyllrb.com/docs/installation/
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Install Bundler and Jekyll
gem install jekyll bundler -
Install dependencies
bundle install -
deploy website
bundle exec jekyll serve
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
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.
- RDMkit
- WorkflowHub project
- RDM Guide
- Infectious Diseases Toolkit
- Applied Bioinformatics and Biostatistics intranet page
- FAIRDOM
- Australian BioCommons How-to-Guides
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
- jQuery Navgoco Menus - Multi-level slide navigation with accordion effect
- Font-Awesome - The famous icon library
- flag-icons - A curated collection of all country flags in SVG + css integration
If you like our work, you can add following badge to the readme of your project:
[](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
The theme is available as open source under the terms of the MIT License.