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README.md
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......@@ -48,5 +48,7 @@ Releases are available via npm at https://www.npmjs.com/package/ebi-framework
## Developing locally
1. Edit any CSS or JS and build with `npm run scss` or `npm run js`
2. Serve index.html with `jekyll serve --port 99`
3. Open http://127.0.0.1:99/EBI-Framework/
2. Serve index.html
- `npm install -g browser-sync`
- `browser-sync start --files index.html --server`
- https://www.browsersync.io/docs/command-line
\ No newline at end of file
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<footer>
<div id="global-footer" class="global-footer">
<nav id="global-nav-expanded" class="global-nav-expanded row">
<!-- Footer will be automatically inserted by footer.js -->
</nav>
<section id="ebi-footer-meta" class="ebi-footer-meta row">
<!-- Footer meta will be automatically inserted by footer.js -->
</section>
</div>
</footer>
<!-- JavaScript -->
<!-- Grab Google CDN's jQuery, with a protocol relative URL; fall back to local if offline -->
<!--
<script>window.jQuery || document.write('<script src="../js/libs/jquery-1.10.2.min.js"><\/script>')</script>
-->
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
<!-- Your custom JavaScript file scan go here... change names accordingly -->
<!-- <script defer="defer" src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/js/script.js"></script> -->
<script defer="defer" src="{{ site.baseurl }}/js/script.js"></script>
<!-- The Foundation theme JavaScript -->
<script src="{{ site.baseurl }}/libraries/foundation-6/js/foundation.js"></script>
<script src="{{ site.baseurl }}/js/foundationExtendEBI.js"></script>
<!-- <script src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/libraries/foundation-6/js/foundation.js"></script> -->
<!-- <script src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/js/foundationExtendEBI.js"></script> -->
<script type="text/JavaScript">$(document).foundation();</script>
<script type="text/JavaScript">$(document).foundationExtendEBI();</script>
{% comment %} Custom global JS could go here: {% endcomment %}
{% for js in site.custom_js %}
<script src="{{js}}"></script>
{% endfor %}
<!-- Google Analytics details... -->
<!-- Change UA-XXXXX-X to be your site's ID -->
<!--
<script>
window._gaq = [['_setAccount','{{site.ga_code}}'],['_trackPageview'],['_trackPageLoadTime']];
Modernizr.load({
load: ('https:' == location.protocol ? '//ssl' : '//www') + '.google-analytics.com/ga.js'
});
</script>
-->
_includes/head.html deleted 100755 → 0
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<head>
<meta charset="utf-8">
<title>{% if page.title %} {{ page.title }} &lt; {% endif %} {{ site.name }} &lt; EMBL-EBI</title>
<meta name="description" content="EMBL-EBI"><!-- Describe what this page is about -->
<meta name="keywords" content="bioinformatics, europe, institute"><!-- A few keywords that relate to the content of THIS PAGE (not the whol project) -->
<meta name="author" content="EMBL-EBI"><!-- Your [project-name] here -->
<meta name="HandheldFriendly" content="true" />
<meta name="MobileOptimized" content="width" />
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="theme-color" content="#70BDBD"> <!-- Android Chrome mobile browser tab color -->
<!-- Add information on the life cycle of this page -->
<meta name="ebi:owner" content="EMBL-EBI Web Development"> <!-- Who should be contacted about changes -->
<meta name="ebi:review-cycle" content="180"> <!-- In days, how often should the content be reviewed -->
<meta name="ebi:last-review" content="2017-12-20"> <!-- The last time the content was reviewed -->
<meta name="ebi:expiry" content="2018-06-20"> <!-- When this content is no longer relevant -->
<!-- For the EMBL global nav (optional) -->
<meta name="embl:rational" content="{{page.embl_rational}}" />
<meta name="embl:external" content="{{page.embl_external}}" />
<meta name="embl:active" content="{{page.embl_active}}" />
<meta name="embl:parent-1" content="{{page.embl_parent_1}}" />
<meta name="embl:parent-2" content="{{page.embl_parent_2}}" />
<!-- If you link to any other sites frequently, consider optimising performance with a DNS prefetch -->
<link rel="dns-prefetch" href="https://ebi.ac.uk" />
<link rel="dns-prefetch" href="https://ebi.emblstatic.net" />
<!-- If you have custom icon, replace these as appropriate.
You can generate them at realfavicongenerator.net -->
<link rel="icon" type="image/x-icon" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/favicon.ico" />
<link rel="icon" type="image/png" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/favicon-32x32.png" />
<link rel="icon" type="image/png" sizes="192×192" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/android-chrome-192x192.png" /> <!-- Android (192px) -->
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/apple-icon-114x114.png"> <!-- For iPhone 4 Retina display (114px) -->
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/apple-icon-72x72.png"> <!-- For iPad (72px) -->
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/apple-icon-144x144.png"> <!-- For iPad retinat (144px) -->
<link rel="apple-touch-icon-precomposed" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/apple-icon-57x57.png"> <!-- For iPhone (57px) -->
<link rel="mask-icon" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/safari-pinned-tab.svg" color="#ffffff"> <!-- Safari icon for pinned tab -->
<meta name="msapplication-TileColor" content="#2b5797"> <!-- MS Icons -->
<meta name="msapplication-TileImage" content="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/images/logos/EMBL-EBI/favicons/mstile-144x144.png">
<!-- CSS: implied media=all -->
<!-- CSS concatenated and minified via ant build script-->
<link rel="stylesheet" href="{{ site.baseurl }}/css/ebi-global.min.css" type="text/css" media="all" />
<!-- <link rel="stylesheet" href="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/css/ebi-global.css" type="text/css" media="all"> -->
<link rel="stylesheet" href="//ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.2/fonts.css" type="text/css" media="none" onload="if(media!=='all')media='all'">
<!-- Use this CSS file for any custom styling -->
<!--
<link rel="stylesheet" href="css/custom.css" type="text/css" media="all">
-->
{% comment %} Custom global CSS could go here: {% endcomment %}
{% for css in site.custom_css %}
<link rel="stylesheet" href="{{css}}">
{% endfor %}
<!-- If you have a custom header image or colour -->
<!--
-->
<meta name="ebi:masthead-color" content="#007c82">
<!-- <meta name="ebi:masthead-image" content="{{ site.domain }}{{ site.baseurl }}/static/background.jpg"> -->
<!-- you can replace this with theme-[projectname].css. See http://www.ebi.ac.uk/web/style/colour for details of how to do this -->
<!-- also inform ES so we can host your colour palette file -->
<link rel="stylesheet" href="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.2/css/theme-embl-petrol.css" type="text/css" media="none" onload="if(media!=='all')media='all'">
<!-- for production the above can be replaced with -->
<!--
<link rel="stylesheet" href="//www.ebi.ac.uk/web_guidelines/css/compliance/mini/ebi-fluid-embl.css">
-->
<!-- end CSS-->
</head>
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<div id="skip-to">
<ul>
<li><a href="#content">Skip to main content</a></li>
</ul>
</div>
<header id="masthead-black-bar" class="clearfix masthead-black-bar">
<!-- Will be populated by script.js -->
<!-- Active item will be set through embl:facet metatags -->
</header>
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{% for node in navigation_list %}
{% if group == null or group == node.group %}
{% if page.url == node.url %}
<li class="active"><a href="{{ site.baseurl }}{{node.url}}" class="active">{{node.title}}</a></li>
{% else %}
<li><a href="{{ site.baseurl }}{{node.url}}">{{node.title}}</a></li>
{% endif %}
{% endif %}
{% endfor %}
{% assign pages_list = nil %}
{% assign group = nil %}
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<ul class="posts">
{% for update in site.posts %}
<li><span>{{ update.date | date_to_string }}</span> » <a href="{{site.baseurl}}/{{ update.url }}" title="{{ update.title }}">{{ update.title }}</a></li>
{% endfor %}
</ul>
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<!DOCTYPE html>
<html lang="en">
{% include head.html %}
<body class="level2"><!-- add any of your classes or IDs -->
{% include local_masthead.html %}
<div id="content" role="main">
<div data-sticky-container>
<div id="masthead" class="masthead" data-sticky data-sticky-on="large" data-top-anchor="main-content-area:top" data-btm-anchor="main-content-area:bottom">
<div class="masthead-inner row">
<!-- local-title -->
<div class="columns medium-7" id="local-title">
<h1><a href="{{ site.domain }}{{ site.baseurl }}" title="Back to {{ site.name }} homepage">{{ page.title }}</a></h1>
</div>
<!-- /local-title -->
<!-- local-nav -->
<nav class="columns">
<ul id="local-nav" class="dropdown menu float-left" data-description="navigational" data-dropdown-menu>
{% comment %}
We construct the site naviagion by loading a list of the site's pages
and filtering to just those with the front matter of:
group: "in_local_navigation"
and we order by adding
order: 2 (whatever number)
{% endcomment %}
{% assign navigation_list = site.pages | sort:"order" %}
{% assign group = 'in_local_navigation' %}
{% include navigation_list.html %}
</ul>
</nav>
<!-- /local-nav -->
</div>
</div>
</div>
<section class="row" id="main-content-area">
<!-- Your menu structure should make a breadcrumb redundant, but if a breadcrump is needed uncomment the below -->
<!--
<nav aria-label="You are here:" role="navigation">
<ul class="breadcrumbs">
<li><a href="#">Home</a></li>
<li><a href="#">Parent</a></li>
<li class="disabled">Disabled</li>
<li>
<span class="show-for-sr">Current: </span> This page
</li>
</ul>
</nav>
-->
<div class="medium-9 columns padding-top-large">
{{ content | markdownify}}
</div>
<div class="medium-3 columns sidebar" data-sticky-container>
</div>
</section>
<!-- Optional local footer (insert citation / project-specific copyright / etc here -->
<!--
<div id="local-footer" class="local-footer">
<div class="row">
<span class="reference">How to reference this page: ...</span>
</div>
</div>
-->
<!-- End optional local footer -->
</div><!-- /.container -->
{% include footer.html %}
</body>
</html>
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---
layout: default
---
<h2>{{ page.title }}</h2>
<p class="meta">{{ page.date | date_to_string }}</p>
<div class="post">
{{ content }}
</div>
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---
layout: default
title: Research sample
embl_rational: 0
embl_external: 0
embl_active: "what:research"
embl_parent_1: "where:ebi"
embl_parent_2: "none"
group: "in_local_navigation"
order: 3
---
## Sample research overview page
index.html
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---
layout: default
title: Project home
embl_rational: 0
embl_external: 0
embl_active: "where:ebi"
embl_parent_1: "none"
embl_parent_2: "none"
group: "in_local_navigation"
order: 1
---
<h2>This is v1.3</h2>
<p>For more information:</p>
<ul>
<li><a href="https://github.com/ebiwd/EBI-Framework/tree/v1.3" class="readmore">Check out the GitHub branch</a></li>
<li><a href="https://github.com/ebiwd/EBI-Framework/issues/103" class="readmore">Read and discuss the roadmap</a></li>
<li><a href="https://github.com/ebiwd/EBI-Framework/issues/103" class="readmore">Join a drop-in clinic</a></li>
<li><a href="http://www.ebi.ac.uk/style-lab/websites/sample-site/" class="readmore">Check out the boilerplate templates</a></li>
</ul>
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8" />
<title>The European Bioinformatics Institute &lt; EMBL-EBI</title>
<meta name="description" content="EMBL-EBI Blank boilerplate page" /><!-- Describe what this page is about -->
<meta name="keywords" content="bioinformatics, europe, institute" /><!-- 3 to 10 keywords about the content of this page (not the whole project) -->
<meta name="author" content="EMBL-EBI" /><!-- Your [project-name] here -->
<meta name="HandheldFriendly" content="true" />
<meta name="MobileOptimized" content="width" />
<meta name="viewport" content="width=device-width,initial-scale=1" />
<meta name="theme-color" content="#70BDBD" /> <!-- Android Chrome mobile browser tab color -->
<!-- Get suggested SEO and social metatags at:
https://www.ebi.ac.uk/style-lab/websites/patterns/meta-copy.html -->
<!-- Add information on the life cycle of this page -->
<meta name="ebi:owner" content="John Doe" /> <!-- Who should be contacted about changes -->
<meta name="ebi:review-cycle" content="30" /> <!-- In days, how often should the content be reviewed -->
<meta name="ebi:last-review" content="2015-12-20" /> <!-- The last time the content was reviewed -->
<meta name="ebi:expiry" content="2016-01-20" /> <!-- When this content is no longer relevant -->
<!-- If you link to any other sites frequently, consider optimising performance with a DNS prefetch -->
<link rel="dns-prefetch" href="//www.ebi.ac.uk" />
<!-- If you have custom icon, replace these as appropriate.
You can generate them at realfavicongenerator.net -->
<link rel="icon" type="image/x-icon" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/favicon.ico" />
<link rel="icon" type="image/png" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/favicon-32x32.png" />
<link rel="icon" type="image/png" sizes="192x192" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/android-chrome-192x192.png" /> <!-- Android (192px) -->
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/apple-icon-114x114.png" /> <!-- For iPhone 4 Retina display (114px) -->
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/apple-icon-72x72.png" /> <!-- For iPad (72px) -->
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/apple-icon-144x144.png" /> <!-- For iPad retinat (144px) -->
<link rel="apple-touch-icon-precomposed" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/apple-icon-57x57.png" /> <!-- For iPhone (57px) -->
<link rel="mask-icon" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/safari-pinned-tab.svg" color="#ffffff" /> <!-- Safari icon for pinned tab -->
<meta name="msapplication-TileColor" content="#2b5797" /> <!-- MS Icons -->
<meta name="msapplication-TileImage" content="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/favicons/mstile-144x144.png" />
<!-- CSS: implied media=all -->
<!-- CSS concatenated and minified via ant build script-->
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/ebi-global.css" type="text/css" media="all" />
<link rel="stylesheet" href="https://dev.ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.2/fonts.css" type="text/css" media="all" />
<!-- Use this CSS file for any custom styling -->
<!--
<link rel="stylesheet" href="css/custom.css" type="text/css" media="all" />
-->
<!-- If you have a custom header image or colour -->
<!--
<meta name="ebi:masthead-color" content="#000" />
<meta name="ebi:masthead-image" content="//www.ebi.ac.uk/web_guidelines/EBI-Framework/images/backgrounds/embl-ebi-background.jpg" />
-->
<!-- you can replace this with theme-[projectname].css. See http://www.ebi.ac.uk/web/style/colour for details of how to do this -->
<!-- also inform ES so we can host your colour palette file -->
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/theme-embl-petrol.css" type="text/css" media="all" />
<!-- end CSS-->
</head>
<body class="level2"><!-- add any of your classes or IDs -->
<div id="skip-to">
<a href="#content">Skip to main content</a>
</div>
<header id="masthead-black-bar" class="clearfix masthead-black-bar">
</header>
<div id="content">
<div data-sticky-container>
<header id="masthead" class="masthead" data-sticky data-sticky-on="large" data-top-anchor="content:top" data-btm-anchor="content:bottom">
<div class="masthead-inner row">
<!-- local-title -->
<div class="columns medium-12" id="local-title">
<h1><a href="../../" title="Back to [service-name] homepage">EBI Framework</a></h1>
</div>
<!-- /local-title -->
<!-- local-nav -->
<nav >
<ul id="local-nav" class="dropdown menu float-left" data-description="navigational">
<li><a href="../../">Overview</a></li>
<li><a data-open="modal-download">Download</a></li>
<li><a href="#">Support <i class="icon icon-generic" data-icon="x"></i></a></li>
</ul>
</nav>
<!-- /local-nav -->
</div>
</header>
</div>
<!-- Suggested layout containers -->
<section id="main-content-area" class="row" role="main">
<!-- Your menu structure should make a breadcrumb redundant, but if a breadcrump is needed uncomment the below -->
<nav aria-label="You are here:" role="navigation">
<ul class="breadcrumbs columns">
<li><a href="../../">EBI Framework</a></li>
<li><a href="../">Sample pages</a></li>
<li>
<span class="show-for-sr">Current: </span> Blank boilerplate
</li>
</ul>
</nav>
<div class="columns">
<section>
<h2>[page-title]</h2>
<p>Your content</p>
</section>
<section>
<h3>Level 3 heading</h3>
<p>More content in a full-width container.</p>
<h4>Level 4 heading</h4>
<p>More content in a full-width container.</p>
</section>
</div>
</section>
<!-- Optional local footer (insert citation / project-specific copyright / etc here -->
<!--
<footer id="local-footer" class="local-footer" role="local-footer">
<div class="row">
<span class="reference">How to reference this page: ...</span>
</div>
</footer>
-->
<!-- End optional local footer -->
</div>
<!-- End suggested layout containers / #content -->
<footer>
<div id="global-footer" class="global-footer">
<nav id="global-nav-expanded" class="global-nav-expanded row">
<!-- Footer will be automatically inserted by footer.js -->
</nav>
<section id="ebi-footer-meta" class="ebi-footer-meta row">
<!-- Footer meta will be automatically inserted by footer.js -->
</section>
</div>
</footer>
<!-- JavaScript -->
<!-- Grab Google CDN's jQuery, with a protocol relative URL; fall back to local if offline -->
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
<!--
<script>window.jQuery || document.write('<script src="../js/libs/jquery-1.10.2.min.js"><\/script>')</script>
-->
<script defer="defer" src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/js/script.js"></script>
<!-- The Foundation theme JavaScript -->
<script src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/libraries/foundation-6/js/foundation.js"></script>
<script src="//ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/js/foundationExtendEBI.js"></script>
<script type="text/JavaScript">$(document).foundation();</script>
<script type="text/JavaScript">$(document).foundationExtendEBI();</script>
<!-- Google Analytics details... -->
<!-- Change UA-XXXXX-X to be your site's ID -->
<script type="text/javascript">!function(e,a,n,t,i,o,c){e.GoogleAnalyticsObject=i,e[i]=e[i]||function(){(e[i].q=e[i].q||[]).push(arguments)},e[i].l=1*new Date,o=a.createElement(n),c=a.getElementsByTagName(n)[0],o.async=1,o.src="//www.google-analytics.com/analytics.js",c.parentNode.insertBefore(o,c)}(window,document,"script",0,"ga"),ga("create","UA-629242-1",{cookieDomain:"auto"}),ga("require","linkid","linkid.js"),ga("set","anonymizeIp",!0),ga("send","pageview");</script>
</body>
</html>
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