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README.md

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

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