This repo is now archived. Content was converted to markdown and mkdocs in the HGVSnomenclature/hgvs-nomenclature repo.

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URL

http://hgvsnomenclature.github.io/VarNomen/ http://varnomen.hgvs.org/

To run

1. Install jekyll
2. gem install --user-install jekyll-redirect-from
   • On Ubuntu, you'll need to apt install ruby-dev
3. Run command jekyll serve --baseurl "" --watch
4. Browser URL: localhost:4000

config.yml

Contains important global site attributes

Attribute	Description
title	Title of every page. i.e. <title>
email	Email for every contact us section
description	Description of the site (shown in the jumbotron on the main page)
baseurl	Root folder, i.e. /VarNomen
url	Base hostname and protocol of site
version	Current version number of the nomenclature
collections	File directories that contain pages for Jekyll to markup
variant-priority	Used when generating order of variants in site structure and display Case-sensitive - use lowercase

All pages

Front matter

last-modified: date Date the page was last modifed. Marked up as "Last modifed: date"

Recommendation pages

Folder Structure

Folder	Contents
/_recommendations	Root
- /sequence	DNA/RNA/protein
- /variant	Holds index page for all recommendations. Definition and Discussion go here
- /description	Description goes here
- /example	Example goes here

###Each recommendation page contains

Category	Notes
Sequence (DNA/RNA/protein)	Maintained in root/sequence/index.html Pages must have layout: recommendation, parent: "sequence" and title: "variant" (in lowercose).
Definition	Maintained in root/sequence/variant/sequence.md as YAML.
Description	Maintained in root/sequence/variant/description/variant-desc.md Pages must have parent: "sequence", title: "variant" (in lowercose) and category: "description"YAML attributes.
Examples	Maintained in root/sequence/variant/example/variant-eg.md Pages must have parent: "sequence", title: "variant" (in lowercose) and category: "example"YAML attributes.
Discussion	Maintained in root/sequence/variant/sequence.md as YAML.

NOTE: variant YAML attributes must be listed in _config.yml under the "variant-priority" list (case-sensitive).

Background Material pages

Root: /_bg-material/

All files maintained as markdown files