inital commit from vicc template

.gitignore

@@ -0,0 +1,4 @@
+_site/
+.sass-cache/
+.jekyll-metadata
+.DS_Store

CNAME

@@ -0,0 +1 @@
+cancervariants.org

Gemfile

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+source 'https://rubygems.org'
+
+gem 'jekyll'
+
+group :jekyll_plugins do
+  gem 'jekyll-gist'
+  gem 'jekyll-paginate'
+  gem "jekyll-asciidoc"
+end
+
+gem 'asciidoctor', '~> 1.5.4'
+gem 'coderay', '1.1.1'
+

Gemfile.lock

@@ -0,0 +1,68 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.5.0)
+      public_suffix (~> 2.0, >= 2.0.2)
+    asciidoctor (1.5.5)
+    coderay (1.1.1)
+    colorator (1.1.0)
+    faraday (0.10.0)
+      multipart-post (>= 1.2, < 3)
+    ffi (1.9.14)
+    forwardable-extended (2.6.0)
+    jekyll (3.3.1)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 1.1)
+      kramdown (~> 1.3)
+      liquid (~> 3.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (~> 1.7)
+      safe_yaml (~> 1.0)
+    jekyll-asciidoc (2.0.1)
+      asciidoctor (>= 1.5.0)
+      jekyll (>= 2.3.0)
+    jekyll-gist (1.4.0)
+      octokit (~> 4.2)
+    jekyll-paginate (1.1.0)
+    jekyll-sass-converter (1.5.0)
+      sass (~> 3.4)
+    jekyll-watch (1.5.0)
+      listen (~> 3.0, < 3.1)
+    kramdown (1.13.0)
+    liquid (3.0.6)
+    listen (3.0.8)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    mercenary (0.3.6)
+    multipart-post (2.0.0)
+    octokit (4.6.2)
+      sawyer (~> 0.8.0, >= 0.5.3)
+    pathutil (0.14.0)
+      forwardable-extended (~> 2.6)
+    public_suffix (2.0.4)
+    rb-fsevent (0.9.8)
+    rb-inotify (0.9.7)
+      ffi (>= 0.5.0)
+    rouge (1.11.1)
+    safe_yaml (1.0.4)
+    sass (3.4.22)
+    sawyer (0.8.1)
+      addressable (>= 2.3.5, < 2.6)
+      faraday (~> 0.8, < 1.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  asciidoctor (~> 1.5.4)
+  coderay (= 1.1.1)
+  jekyll
+  jekyll-asciidoc
+  jekyll-gist
+  jekyll-paginate
+
+BUNDLED WITH
+   1.13.6

LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2015 The Griffith Lab
+Copyright (c) 2017 The McDonnell Genome Institute
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.md

@@ -1,2 +1,16 @@
-# griffithlab.github.io
-Griffith lab research website
+## Overview
+
+This is the github repo for the griffith lab [website](http://griffithlab.org). The website uses the static site generator [jekyll](https://jekyllrb.com/) and is based on the [Feeling Responsive jekyll theme](https://github.com/Phlow/feeling-responsive). Development occurs on the master branch, the live site is located on the gh-pages branch.
+
+## Installation
+
+To install this site locally run the following commands:
+
+1. Clone the repo and cd into it `$ git clone [email protected]:griffithlab/griffithlab.github.io.git`
+2. Install the bundler `$ gem install bundler`
+3. Install gems `$ bundle install`
+4. run jekyll and watch for changes `$ bundle exec jekyll serve --config _config.yml,_config_dev.yml --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.

_config.yml

@@ -0,0 +1,275 @@
+# ASCII-Font › http://patorjk.com/software/taag/#p=display&f=Slant&t=Phlow
+#
+#      _____ _ __          _____      __  __  _
+#     / ___/(_) /____     / ___/___  / /_/ /_(_)___  ____ ______
+#     \__ \/ / __/ _ \    \__ \/ _ \/ __/ __/ / __ \/ __ `/ ___/
+#    ___/ / / /_/  __/   ___/ /  __/ /_/ /_/ / / / / /_/ (__  )
+#   /____/_/\__/\___/   /____/\___/\__/\__/_/_/ /_/\__, /____/
+#                                                 /____/
+#
+# Title of your website
+title: 'Griffith Lab'
+
+# The slogan describes your website and is used on homepage in <title> and other important places
+slogan: ''
+
+# The description is used on homepage and in the footer to quickly describe your website. Use a maximum of 150 characters for SEO-purposes.
+description: 'This is the website for the academic lab of Malachi and Obi Griffith'
+
+# The credits show up in the includes/_footer.html – It would be nice of you to leave a link to Phlow or Feeling Responsive as a thank you :)
+credits: '<p>Powered by <a href="http://jekyllrb.com/" target="_blank">Jekyll</a> based on the theme <a href="http://phlow.github.io/feeling-responsive/">Feeling Responsive</a>.</p>'
+
+# Main author of the website
+# See > authors.yml
+author: Obi Griffith, Malachi Griffith
+
+# This URL is the main address for absolute links. Don't include a slash at the end.
+#
+url: 'http://griffithlab.org'
+#baseurl: '/vicc', this breaks github pages for some reason, investigate, ZL
+
+
+# This is for the editing function in _/includes/improve_content
+# Leave it empty if your site is not on GitHub/GitHub Pages
+improve_content: https://github.com/griffithlab/griffithlab.github.io/edit/master/
+
+# This URL points directly to the images directory making
+# things easier to link to images in posts and templates. It needs a slash at the end.
+#
+# Example: <img src="{{ site.urlimg }}{{ post.image.title }}" />
+# Markdown-Example for posts ![Image Text]({{ site.urlimg }}image.jpg)
+#
+urlimg: 'http://griffithlab.org/images/'
+
+
+# Logo size is 600x80 pixels
+logo: "VICC_no_text_mint.png"
+
+# Gems
+gems:
+    - jekyll-asciidoc
+    - jekyll-gist
+    - jekyll-paginate
+
+
+#       ____              _             __  _
+#      / __ \____ _____ _(_)___  ____ _/ /_(_)___  ____
+#     / /_/ / __ `/ __ `/ / __ \/ __ `/ __/ / __ \/ __ \
+#    / ____/ /_/ / /_/ / / / / / /_/ / /_/ / /_/ / / / /
+#   /_/    \__,_/\__, /_/_/ /_/\__,_/\__/_/\____/_/ /_/
+#               /____/
+#
+# add back in blog folder to re-enable
+##paginate: 5                      # Paginates all X entries
+# paginate_path: "blog/page:num"   # Pagination path › Important for blog page in /blog/ to work
+
+
+# Theme works best with Kramdown (using the table of contents function)
+markdown: kramdown
+permalink: /:categories/:title/
+highlight: rouge
+excerpt_separator: "<!--more-->"
+include: ['.htaccess']
+# Exclude these files from your production _site
+exclude:
+    - .sass-cache
+    - Gemfile
+    - Gemfile.lock
+    - LICENSE
+    - README.md
+    - INSTALL.md
+    - .gitignore
+    - .DS_Store
+
+
+# The language setting is used in /includes/header.html for html-settings
+language: 'en'
+
+
+# Used › default.html front-matter and compress.html
+# Options › http://jch.penibelst.de
+compress_html:
+  clippings: all
+  comments: ["<!-- ", " -->"]
+  endings: all
+  profile: false
+  ignore:
+    envs: [development]
+
+
+#
+#       ____       ____            ____
+#      / __ \___  / __/___ ___  __/ / /_
+#     / / / / _ \/ /_/ __ `/ / / / / __/
+#    / /_/ /  __/ __/ /_/ / /_/ / / /_
+#   /_____/\___/_/  \__,_/\__,_/_/\__/
+#
+# Default Settings
+
+defaults:
+  -
+    scope:
+      path: '' 				# an empty string here means all files in the project
+      type: 'pages'
+    values:
+      show_meta: false 	# Hide metadata for all pages
+      # sidebar:    		# Possible values › left, right › by default there will be no sidebar
+      comments: false
+      author: Griffith     # Default author for pages
+  -
+    scope:
+      path: ''
+      type: 'posts'
+    values:
+      show_meta: true   # Show metadata for all posts
+      # sidebar:        # Possible values › left, right › by default there will be no sidebar
+      comments: false
+      author: Griffith     # Default author for posts
+
+
+
+#       _   __            _             __  _
+#      / | / /___ __   __(_)___ _____ _/ /_(_)___  ____
+#     /  |/ / __ `/ | / / / __ `/ __ `/ __/ / __ \/ __ \
+#    / /|  / /_/ /| |/ / / /_/ / /_/ / /_/ / /_/ / / / /
+#   /_/ |_/\__,_/ |___/_/\__, /\__,_/\__/_/\____/_/ /_/
+#                       /____/
+#
+#  Open _data/navigation.yml to adjust the left and right topbar navigation
+#
+
+
+
+#     _____ __________
+#    / ___// ____/ __ \
+#    \__ \/ __/ / / / /
+#   ___/ / /___/ /_/ /
+#  /____/_____/\____/    Verify Website to Webmaster Tools
+
+# google_author:             ''
+# google_site_verification:  ''
+# bing_webmastertools_id:    ''
+# yandex_site_verification:  ''
+# alexa_verify_id:           ''
+
+
+
+#       ______            _
+#      / ____/___ __   __(_)________  ____  _____
+#     / /_  / __ `/ | / / / ___/ __ \/ __ \/ ___/
+#    / __/ / /_/ /| |/ / / /__/ /_/ / / / (__  )
+#   /_/    \__,_/ |___/_/\___/\____/_/ /_/____/   Favicon-Crap: Favicons, Chrome, Android & Apple Touch Buttons
+#                                                 More information » https://mathiasbynens.be/notes/touch-icons
+
+favicon-32x32:                          'favicon-32x32.png'
+touch-icon-192x192:                     'touch-icon-192x192.png'
+apple-touch-icon-180x180-precomposed:   'apple-touch-icon-180x180-precomposed.png'
+apple-touch-icon-152x152-precomposed:   'apple-touch-icon-152x152-precomposed.png'
+apple-touch-icon-144x144-precomposed:   'apple-touch-icon-144x144-precomposed.png'
+apple-touch-icon-120x120-precomposed:   'apple-touch-icon-120x120-precomposed.png'
+apple-touch-icon-114x114-precomposed:   'apple-touch-icon-114x114-precomposed.png'
+apple-touch-icon-76x76-precomposed:     'apple-touch-icon-76x76-precomposed.png'
+apple-touch-icon-72x72-precomposed:     'apple-touch-icon-72x72-precomposed.png'
+apple-touch-icon-precomposed:           'apple-touch-icon-precomposed.png'
+msapplication_tileimage:                'msapplication_tileimage.png'               # Size 144x144
+msapplication_tilecolor:                '#fabb00'
+
+
+#       ______                __                __
+#      / ____/___ _________  / /_  ____  ____  / /__
+#     / /_  / __ `/ ___/ _ \/ __ \/ __ \/ __ \/ //_/
+#    / __/ / /_/ / /__/  __/ /_/ / /_/ / /_/ / ,<
+#   /_/    \__,_/\___/\___/_.___/\____/\____/_/|_|      Facebook-Optimization › http://j.mp/fb_optimize
+
+# og_image:                           'http://images.phlow.de/phlow/phlow_de-logo-512x.png'
+# og_locale:                          'en_EN'
+# og_type:                            'website'
+
+
+#      _____            _       __   __  ___         ___
+#     / ___/____  _____(_)___ _/ /  /  |/  /__  ____/ (_)___ _
+#     \__ \/ __ \/ ___/ / __ `/ /  / /|_/ / _ \/ __  / / __ `/
+#    ___/ / /_/ / /__/ / /_/ / /  / /  / /  __/ /_/ / / /_/ /
+#   /____/\____/\___/_/\__,_/_/  /_/  /_/\___/\__,_/_/\__,_/
+#
+#  Open _data/socialmedia.yml to adjust the left and right topbar navigation
+#
+
+#socialmedia:
+#    twitter:
+
+
+#        ____  _
+#       / __ \(_)________ ___  _______
+#      / / / / / ___/ __ `/ / / / ___/
+#     / /_/ / (__  ) /_/ / /_/ (__  )
+#    /_____/_/____/\__, /\__,_/____/
+#                    /_/
+#
+# used in _includes/comments
+
+# disqus_shortname: vicc
+
+
+#      _____
+#     / ___/____ ___________
+#     \__ \/ __ `/ ___/ ___/
+#    ___/ / /_/ (__  |__  )     More › http://sass-lang.com/
+#   /____/\__,_/____/____/      More › http://jekyllrb.com/docs/assets/#sassscss
+#
+
+sass:
+    sass_dir: _sass
+    style: :compressed
+
+
+#       ___                __      __  _
+#      /   |  ____  ____ _/ /_  __/ /_(_)_________
+#     / /| | / __ \/ __ `/ / / / / __/ / ___/ ___/
+#    / ___ |/ / / / /_/ / / /_/ / /_/ / /__(__  )
+#   /_/  |_/_/ /_/\__,_/_/\__, /\__/_/\___/____/      https://www.google.com/analytics/
+#                        /____/
+#
+# used in _includes/footer_scripts
+
+google_analytics_tracking_id: ""
+
+
+
+#   _                 _     _
+#  | |_ __ ___      _| | __| |_ ___
+#  | __/ _` \ \ /\ / / |/ /| __/ _ \
+#  | || (_| |\ V  V /|   < | || (_) |
+#   \__\__,_| \_/\_/ |_|\_(_)__\___/     More › https://www.tawk.to/knowledgebase/
+#
+#  tawk.to is a free live chat app that lets you monitor and chat
+#  with visitors on your website or from a free customizable page
+#
+#  To load the script add tawkto: true in front matter of each page
+#
+# used in _includes/footer_scripts
+
+# tawkto_embed_uri:
+
+
+#     ___              _     __           __
+#    /   |  __________(_)___/ /___  _____/ /_____  _____
+#   / /| | / ___/ ___/ / __  / __ \/ ___/ __/ __ \/ ___/
+#  / ___ |(__  ) /__/ / /_/ / /_/ / /__/ /_/ /_/ / /
+# /_/  |_/____/\___/_/\__,_/\____/\___/\__/\____/_/
+#
+#  Asciidoctor is a fast text processor and publishing toolchain for converting
+#  AsciiDoc content to HTML5, DocBook 5 (or 4.5) and other formats.
+#
+#  https://github.com/asciidoctor/jekyll-asciidoc
+#  https://github.com/asciidoctor
+#
+#
+
+asciidoctor-enabled: false
+asciidoctor:
+  description: testtewtetrue
+  attributes:
+    source-highlighter: coderay
+    coderay-css: style
+    icons: font