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Overview

This is the github repo for the RNA-Seq Workshop website. The website uses the static site generator jekyll and is based on the Alembic theme. Development occurs on the dev branch, the live site is located on the master branch.

Installation

To install this site locally run the following commands:

  1. Clone the repo and cd into it $ git clone [email protected]:griffithlab/rnabio.org.git
  2. Install the bundler $ gem install bundler
  3. Install gems $ bundle install
  4. run jekyll and watch for changes $ bundle exec jekyll serve --watch

The site should now be running on localhost port 4000. Changes to files will show up interactively on localhost:4000

Note: The _config.yml file is only read during the initial serve, changing this file will require re-running step 4 for changes to appear.

Docker Installation

To install the site locally with docker run the following commands:

  1. Clone the repo $ git clone [email protected]:griffithlab/rnabio.org.git
  2. Pull the docker image $ docker pull griffithlab/rnabiodev:0.0.3
  3. Run the docker $ docker run -p 4000:4000 -v ~/git/rnabio.org/:/opt/git/rnabio.org -it griffithlab/rnabiodev:0.0.3

Make sure that the above command has correct path to cloned git repo (The first part specified with -v option). The site should now be running on localhost port 4000. Changes to files will show up interactively on localhost:4000.

Note: The Dockerfile for this image is maintained in this repo and the image itself is hosted on dockerhub.

Note: The _config.yml file is only read during the initial serve, changing this file will require re-running step 3 for changes to appear.

Adding Course Content

Course content is located in the _posts directory, course pages must be named following the format: year-month-day-name.md for example 0000-00-00-name.md. This naming is important for ordering course content, further the front matter tag in the markdown file should include date as well for the same reason. Additional useful tags are categories for locating a course in a specific module. An example of front matter tags in a markdown file is supplied below:

---
title: Introduction to RNA-Seq
categories:
    - Day 1
feature_image: "https://unsplash.it/1200/400?image=200"
date: 0001-01-01
---

Adjusting The Navigation Header and Pages

The Navigation Header is defined in the _config.yml file. Navigation header pages are markdown files and are located in the root directory. For example the about page is located at /about.md. All markdown files should have front matter tags, see jekyll docs.

_layouts and Page Display

In General all markdown files should have a layout: front matter tag. The exception to this are files in the _posts directory which default to a post layout format. Layouts are defined in the _layouts directory which consist of html files specifying content. Jekyll uses liquid templating and this syntax is commonly seen throughout these html pages. A command such as {% include post-list.html %} will look in the _includes directory and add in the html content for post-list.html.

Hints and Tips

License

The code base for this website originates from the alembic jekyll theme by David Darnes and is licensed under an MIT license. Course content, is licensed under CC-BY-SA 4.0 unless otherwise stated.