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_config.yml
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_config.yml
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# Site configuration
# 1. Files excluded from Jekyll builds
# 2. Installed Gems
# 3. Gem settings
# 4. Jekyll settings
# 5. Collections
# 6. Jekyll collections settings
# 7. Site settings
# 8. Site navigation
# 1. Files excluded from Jekyll builds
exclude:
- README.md
- LICENSE
- CNAME
- Gemfile
- Gemfile.lock
- alembic-jekyll-theme.gemspec
- assets/lectures
- assets/course_scripts
- .swp
# 2. Installed Gems
plugins:
- jekyll-sitemap
- jekyll-mentions
- jekyll-paginate
- jekyll-seo-tag
- jekyll-redirect-from
- jekyll-feed
- jemoji
# 3. Gem settings
paginate: 2 # jekyll-paginate > items per page
paginate_path: blog/page:num # jekyll-paginate > blog page
jekyll-mentions: https://twitter.com # jekyll-mentions > service used when @replying
twitter:
username: zlskidmore # jekyll-seo-tag > Owners twitter username
author: Zachary Skidmore # jekyll-seo-tag > default author
social: # jekyll-seo-tag > social overrides
name: Zachary Skidmore # jekyll-seo-tag > real name
links: # jekyll-seo-tag > social aliases (sameAs)
- https://twitter.com/zlskidmore
- https://github.com/zlskidmore
# 4. Jekyll settings
sass:
style: compressed # Style compression
permalink: pretty # Permalink style (/YYYY/MM/DD/page-name/)
excerpt_separator: <!-- more --> # Marks end of excerpt in posts
timezone: UTC # Timezone for blog posts and alike
# 5. Collections
collections:
posts:
title: Posts # Needed for Siteleaf
output: true
description: "My thoughts and ideas" # The post list page content
feature_text: |
Welcome to the blog
feature_image: "assets/genvis-dna-bg_optimized_v1a.png"
# 6. Jekyll collections settings
defaults:
-
scope:
path: ""
type: pages
values:
layout: page # Default layout
image: "/assets/logos/DNA.jpg" # Default image for sharing
-
scope:
path: ""
type: posts
values:
layout: post # Default layout
image: "/assets/logos/DNA.jpg" # Default image for sharing
# 7. Site settings
encoding: utf-8 # Make sure the encoding is right
title: "Griffith Lab" # Site name or title, also used in jekyll-seo-tag
logo: "/assets/logos/Site_Logo3_v2.png" # Site logo, also used in jekyll-seo-tag
logo_link: "http://www.griffithlab.org"
description: "The RNAbio.org site is meant to accompany RNA-seq workshops delivered at various times during the year at various places (New York, Toronto, Germany, Glasgow, etc) in collaboration with various bioinformatics workshop organizations (CSHL, CBW, Physalia, PR Informatics, etc.). It can also be used as a standalone online course. The goal of the resource is to provide a comprehensive introduction to RNA-seq, NGS data, bioinformatics, cloud computing, BAM/BED/VCF file format, read alignment, data QC, expression estimation, differential expression analysis, reference-free analysis, data visualization, transcript assembly, etc." # Site description and default description, also used in jekyll-seo-tag
url: "http://www.rnabio.org/" # Site url, also used in jekyll-seo-tag
baseurl: ""
repo: "https://github.com/griffithlab/rnabio.org"
email: "[email protected]"
avatarurl: "/assets/logos/DNA.jpg"# Uses avatars for favicons to get multple sites, eg Gravatar, Twitter, GitHub
# Silence warnings caused by jekyll-sass-converter-3.0.0 until Jekyll is updated
# For details: https://github.com/jekyll/minima/issues/709
sass:
quiet_deps: true
# 8. Site navigation
navigation_header:
Home: /
Course: /course/
Schedule: /schedule/
Authors: /authors/
Resources: /resources/
Acknowledgments: /acknowledgements/
Search: /search/
navigation_footer:
McDonnell Genome Institute - Washington University: http://genome.wustl.edu/
contact_obi:
twitter: https://twitter.com/obigriffith
github: https://github.com/obigriffith
link: https://griffithlab.org/
contact_malachi:
twitter: https://twitter.com/malachigriffith
github: https://github.com/malachig
link: https://griffithlab.org/
contact_brian:
twitter: https://twitter.com/brianjhaas
github: https://github.com/brianjohnhaas
contact_allegra:
link: https://sites.wustl.edu/pettilab/
contact_aaron:
twitter: https://twitter.com/aaronquinlan
github: https://github.com/arq5x
link: http://quinlanlab.org/
contact_jason:
github: https://github.com/jasonwalker80
contact_alex:
twitter: https://twitter.com/handlerwagner
github: https://github.com/ahwagner
link: http://alexwagner.info/
contact_kelsy:
twitter: https://twitter.com/kelsy_cotto
github: https://github.com/kcotto
contact_zach:
twitter: https://twitter.com/zlskidmore
github: https://github.com/zlskidmore
contact_chris:
twitter: https://twitter.com/chrisamiller
github: https://github.com/chrisamiller
contact_megan:
github: https://github.com/mrichters
social_links:
#Twitter:
#LinkedIn:
#Google+:
GitHub: https://github.com/griffithlab/rnabio.org
#link:
sharing_links:
#Twitter: "#1DA1F2"
#facebook: "#3B5998"
#Google+: "#DC4E41"
#Reddit: "#FF4500"