legumeinfo.org

This repository holds the Jekyll site hosted at www.legumeinfo.org.

Commits to the main branch will trigger a GitHub Action workflow that build the static site & deploy to the jekyll-stage.legumeinfo.org branch. This branch is hosted via GitHub Pages at https://jekyll-stage.legumeinfo.org.

When a tag is pushed, a GitHub Action workflow will build the static site & deploy to the legumeinfo/legumeinfo.org repository (www.legumeinfo.org branch). This branch is hosted via GitHub Pages at https://www.legumeinfo.org (requests for https://legumeinfo.org will redirect to https://www.legumeinfo.org).

The site is styled using a custom UIkit theme, which requires UIkit's SCSS files. As such, UIkit is a submodule of this repository and must be cloned with the repository:

git clone --recurse-submodules https://github.com/legumeinfo/jekyll-legumeinfo.git

Running the Site

The following methods will run the site on your computer at http://localhost:4000. Changes made will be immediately reflected in the browser due to LiveReload.

Ruby

You can run the site with Ruby as follows:

gem install bundler jekyll
bundle install
bundle exec jekyll serve

Docker

You can run the site with Docker as follows:

docker-compose up -d

Theme

This site uses a modified version of the Legume Information System Jekyll theme.

News Posts

News posts are plain text markdown with a YAML header, created by adding a file under news/_posts/ with a name of the format yyyy-mm-dd-unique-identifier.md. For example:

---
layout: news-item
title: Tepary bean genomes added to LIS
author: Sam Hokin
date: 2021-10-01 17:00
summary: Phaseolus acutifolius (tepary bean) added to LIS
---
[Phaseolus acutifolius (tepary bean)](/taxa/phaseolus) is a drought- and heat-tolerant crop
native to the American Southwest and Mexico; it joins the growing set of annotated genomes at LIS,
with a cultivated and wild accession described in [Moghaddam et al. 2021](https://doi.org/10.1038/s41467-021-22858-x).
The cultivated accession has been added as the primary representative of the species.

You can place blank lines in the content to generate paragraphs. Images are not supported in news items.

Blog Posts

Blog posts are created by adding a file named blog/_posts/yyyy-mm-dd-unique-identifier.md.

A blog post has a YAML header which provides key information. For example, a post with the filename 2018-09-10-macrosynteny-gcv.md has the following header:

---
layout: blog-item
title: Bringing Macrosynteny to the GCV Multi-view
author: Andrew Farmer
date: 2018-09-10
summary: The multi-alignment view of the Genome Context Viewer has been updated to support visualization of multi-way macrosynteny between the chromosomes from which microsyntenic segments were taken.
---

The resulting blog URL generated for this post is then /blog/2018/09/10/macrosynteny-gcv.html. The main /blog page provides a list of blog posts, most recent first.

The blog content is plain text entered below the header. Blank lines will generate paragraph tags in the generated HTML as you'd wish. However, a bit more work is required to place images in your post:

• place the image file under assets/img/blog_images/
• use the normal HTML img tag in your content
• wrap the image inside a blog-image div (so we have consistent placement, margins, and border)
• wrap optional attribution in a attribution div below the image

Here's an example of a short post with an image which includes attribution:

The Genomic Context Viewer (GCV) is a web application that provides interactive and synchronized comparative genomics visualizations.

<div class="blog-image">
  <img src="/assets/img/blog_images/instructions-gcv.gif" alt="Screen capture of the GCV user interface"/>
  <div class="attribution">&copy; 2018 NCGR</div>
</div>

Comparisons are performed by determining conservation of gene order and orientation across related species or individuals using homology based on gene family assignments....