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Initializing bioSyntax.org website
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‎.gitignore

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_site
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.DS_Store
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*.sublime-project
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*.sublime-workspace
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codekit-config.json
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node_modules
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Gemfile.lock
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.sass-cache
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.jekyll-metadata
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local

‎.jshintrc

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{
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"bitwise": true,
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"browser": true,
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"curly": true,
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"eqeqeq": true,
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"eqnull": true,
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"es5": false,
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"esnext": true,
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"immed": true,
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"jquery": true,
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"latedef": true,
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"newcap": true,
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"noarg": true,
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"node": true,
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"strict": false,
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"trailing": false,
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"undef": true,
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"multistr": true,
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"expr": true
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}

‎404.md

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---
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layout: page
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title: "Page Not Found"
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description: "Page not found. Your pixels are in another canvas."
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comments: false
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share: false
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permalink: /404.html
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---
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Sorry, but the page you were trying to view does not exist --- perhaps you can try searching for it below.
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<script type="text/javascript">
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var GOOG_FIXURL_LANG = 'en';
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var GOOG_FIXURL_SITE = '{{ site.url }}'
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</script>
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<script type="text/javascript"
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src="//linkhelp.clients.google.com/tbproxy/lh/wm/fixurl.js">
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</script>

‎Gemfile

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source "https://rubygems.org"
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gem "json"
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gem "jekyll"
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gem "jekyll-sitemap"
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gem "jekyll-feed"
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gem "jekyll-paginate"
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gem "jekyll-gist"
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gem "jekyll-redirect-from"

‎Gruntfile.js

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'use strict';
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module.exports = function(grunt) {
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grunt.initConfig({
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jshint: {
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options: {
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jshintrc: '.jshintrc'
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},
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all: [
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'Gruntfile.js',
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'!assets/js/*.js',
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'!assets/js/plugins/*.js',
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'!assets/js/scripts.min.js'
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]
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},
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uglify: {
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dist: {
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files: {
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'assets/js/scripts.min.js': [
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'assets/js/plugins/*.js',
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'assets/js/_*.js'
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]
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}
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}
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},
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imagemin: {
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dist: {
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options: {
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optimizationLevel: 7,
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progressive: true
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},
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files: [{
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expand: true,
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cwd: 'images/',
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src: '{,*/}*.{png,jpg,jpeg}',
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dest: 'images/'
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}]
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}
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},
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svgmin: {
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dist: {
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files: [{
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expand: true,
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cwd: 'images/',
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src: '{,*/}*.svg',
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dest: 'images/'
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}]
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}
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},
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watch: {
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js: {
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files: [
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'<%= jshint.all %>'
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],
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tasks: ['jshint','uglify']
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}
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},
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clean: {
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dist: [
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'assets/js/scripts.min.js'
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]
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}
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});
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// Load tasks
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grunt.loadNpmTasks('grunt-contrib-clean');
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grunt.loadNpmTasks('grunt-contrib-jshint');
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grunt.loadNpmTasks('grunt-contrib-uglify');
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grunt.loadNpmTasks('grunt-contrib-watch');
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grunt.loadNpmTasks('grunt-contrib-imagemin');
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grunt.loadNpmTasks('grunt-svgmin');
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// Register tasks
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grunt.registerTask('default', [
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'clean',
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'uglify',
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'imagemin',
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'svgmin'
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]);
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grunt.registerTask('dev', [
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'watch'
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]);
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};

‎LICENSE

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The MIT License (MIT)
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Copyright (c) 2017 Artem Babaian
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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## HPSTR Jekyll Theme Elements
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The MIT License (MIT)
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Copyright (c) 2014 Michael Rose
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎_config.yml

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title: bioSyntax
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description: Syntax Highlighting for Computational Biology
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disqus_shortname:
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reading_time: false
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words_per_minute: 200
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# Your site's domain goes here (eg: https://mmistakes.github.io, http://yourdomain.com, etc)
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# When testing locally leave blank or use http://localhost:4000
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url: http://localhost:4000
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# Owner/author information
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owner:
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name: bioSyntax
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avatar: atcg.png
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bio: "Syntax Highlighting for Computational Biology"
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email: [email protected]
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# Social networking links used in footer. Update and remove as you like.
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twitter:
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facebook:
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github: ababaian/bioSyntax
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stackexchange:
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linkedin:
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instagram:
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flickr:
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tumblr:
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# google plus id, include the '+', eg +mmistakes
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google_plus:
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# Background image to be tiled on all pages
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background:
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# Analytics and webmaster tools stuff goes here
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google_analytics:
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google_verify:
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# https://ssl.bing.com/webmaster/configure/verify/ownership Option 2 content= goes here
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bing_verify:
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# http://en.wikipedia.org/wiki/List_of_tz_database_time_zones
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timezone: America/Vancouver
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future: true # publish future dated posts -- true, false (default)
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highlighter: rouge
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markdown: kramdown
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plugins:
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- jekyll-sitemap
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- jekyll-paginate
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- jekyll-gist
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- jekyll-redirect-from
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# - jekyll-feed
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sass:
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sass_dir: _sass
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style: compressed
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# https://github.com/mojombo/jekyll/wiki/Permalinks
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#permalink: /:categories/:title/
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# Amount of post to show on home page
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paginate: 5
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kramdown:
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input: GFM
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auto_ids: true
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footnote_nr: 1
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entity_output: as_char
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toc_levels: 1..6
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enable_coderay: false
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include:
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- .htaccess
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exclude:
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- "*.less"
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- "*.sublime-project"
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- "*.sublime-workspace"
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- .asset-cache
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- .bundle
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- .jekyll-assets-cache
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- .sass-cache
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- CHANGELOG
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- Capfile
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- Gemfile
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- Gruntfile.js
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- LICENSE
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- README
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- Rakefile
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- config
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- gulpfile.js
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- lib
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- log
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- node_modules
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- package.json
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- spec
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- tmp
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- local

‎_data/navigation.yml

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# Menu navigation links
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- title: Theme Setup
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url: /theme-setup/
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- title: External Link
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url: http://mademistakes.com

‎_includes/browser-upgrade.html

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<!--[if lt IE 9]><div class="upgrade"><strong><a href="http://whatbrowser.org/">Your browser is quite old!</strong> Why not upgrade to a different browser to better enjoy this site?</a></div><![endif]-->

‎_includes/disqus_comments.html

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{% if site.disqus_shortname %}
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<script type="text/javascript">
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/* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
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var disqus_shortname = '{{ site.disqus_shortname }}'; // required: replace example with your forum shortname
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/* * * DON'T EDIT BELOW THIS LINE * * */
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(function() {
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var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
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dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
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(document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
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})();
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/* * * DON'T EDIT BELOW THIS LINE * * */
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(function () {
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var s = document.createElement('script'); s.async = true;
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s.type = 'text/javascript';
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s.src = '//' + disqus_shortname + '.disqus.com/count.js';
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(document.getElementsByTagName('HEAD')[0] || document.getElementsByTagName('BODY')[0]).appendChild(s);
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}());
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</script>
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<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
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<a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a>
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{% endif %}

‎_includes/feed-footer.html

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&lt;p&gt;&lt;a href=&quot;{{ site.url }}{{ post.url }}&quot;&gt;{{ post.title | xml_escape }}&lt;/a&gt; was last updated on {{ post.date | date: "%B %d, %Y" }}.&lt;/p&gt;

‎_includes/footer.html

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<!-- <span>&copy; {{ site.time | date: '%Y' }} {{ site.owner.name }}. Powered by <a href="http://jekyllrb.com" rel="nofollow">Jekyll</a> using the <a href="https://mademistakes.com/work/hpstr-jekyll-theme/" rel="nofollow">HPSTR Theme</a>.</span> -->
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<span> <a href="mailto:{{ site.owner.email }}">Contact us: <i class="fa fa-fw fa-envelope"></i></a> &ensp;|&ensp;
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<a href="https://github.com/{{ site.owner.github }}">Source: <\></a> &ensp;|&ensp;
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<a href="http://www.hackseq.com"><img src="{{ site.url }}/images/hackseq_project_tag.png"></a>
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</span>

‎_includes/gallery

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{% assign images = include.images | split:" " %}
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{% assign caption = include.caption %}
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{% assign cols = include.cols %}
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{% case cols %}
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{% when 1 %}
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{% assign class = "" %}
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{% when 2 %}
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{% assign class = "half" %}
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{% when 3 %}
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{% assign class = "third" %}
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{% else %}
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{% assign class = "" %}
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{% endcase %}
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<figure {% if class != "" %}class="{{ class }}"{% endif %}>
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{% for image in images %}
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<a href="{{ image }}"><img src="{{ image }}" alt=""></a>
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{% endfor %}
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<figcaption>{{ caption }}</figcaption>
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</figure>

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