Commit 9a2c8f66 authored by Yohan Jarosz's avatar Yohan Jarosz

add frozen pages system

parent ba8949cb
......@@ -4,3 +4,4 @@ _site
!/projects/index.md
/web/*
!/web/.gitkeep
!/web/index.md
<br/>
<br/>
<div class="well">
<div class="row">
<div class="col-xs-12 col-md-6">
<a href="/frozen/index.html">Back to frozen pages</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-6">
<a href="http://r3lab.uni.lu">R3lab homepage</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-6">
Copyright © <a href="http://www.uni.lu" target="_blank">Université du Luxembourg</a> 2015. All rights reserved.
</div>
</div>
</div>
<script src="/js/jquery-1.11.3.min.js"></script>
<script src="/js/bootstrap.min.js"></script>
......@@ -9,21 +9,21 @@
<div class="container-fluid">
{% if page.index %}
{% assign brand = page.index | split:"$" %}
<a class="navbar-brand" href="{{ site.baseurl }}/web/{{brand[0]}}">{{brand[1]}}</a>
<a class="navbar-brand" href="{{ site.baseurl }}{{brand[0]}}">{{brand[1]}}</a>
{% endif %}
<ul class="nav navbar-nav">
{% if page.nav %}
{% capture indexurl %}/web/{{brand[0]}}/{% endcapture %}
{% capture indexurl %}{{brand[0]}}index.html{% endcapture %}
{% assign navs = page.nav | split:"," %}
{% for nav in navs %}
{% assign link = nav | split:"$" %}
{% assign myurl = link[0] %}
{% if myurl contains '://' %}
<li class="{% if page.url contains myurl %}active{% endif %}"><a href="{{myurl}}">{{link[1]}}</a></li>
{% elsif myurl == 'index' and page.url == indexurl %}
{% elsif myurl == '/index' and page.url == indexurl %}
<li class="active"><a href="{{myurl}}.html">{{link[1]}}</a></li>
{% else %}
<li class="{% if page.url contains myurl %}active{% endif %}"><a href="{{myurl}}.html">{{link[1]}}</a></li>
<li class="{% if page.url contains myurl and myurl != '/index' and myurl != 'index' %}active{% endif %}"><a href="{{myurl}}.html">{{link[1]}}</a></li>
{% endif %}
{% endfor %}
</ul>
......
<!DOCTYPE html>
<html>
{% include head.html %}
<body>
<div class="container">
{% include header.html %}
{{ content }}
{% include frozenfooter.html %}
</div>
</body>
</html>
---
layout: default
---
<div class="container">
<div>{{ content }}</div>
</div>
<div>{{ content }}</div>
---
layout: frozen
index: /frozen/imp.html$Integrated Metaomic Pipeline
nav: /frozen/imp$Home,/frozen/index$R3Lab frozen pages
theme: paper
type: frozen
title: Frozen IMP
description: <b>I</b>ntegrated <b>M</b>etaomic <b>P</b>ipeline
---
<style>
.reproblock {
margin-bottom: 50px;
padding: 10px 30px 10px 30px;
border: 1px solid darkgrey;
}
.reproblocktitle {
margin-bottom: 50px;
padding: 30px;
border: 1px solid darkgrey;
}
.rfixed {
height: 330px;
}
.reproblocktitle rtitle {
font-size: 15px;
text-transform: uppercase;
text-align: center;
color: black;
margin: 8px;
padding: 0px;
height: inherit;
}
.reproblocktitle rdoi {
font-size: 15px;
text-align: center;
color: black;
margin: 8px;
padding: 0px;
height: inherit;
}
.reproblock rtitle {
font-size: 15px;
text-transform: uppercase;
text-align: center;
color: black;
margin: 8px;
padding: 0px;
height: inherit;
}
.reproblock rbody {
display: inline-block;
vertical-align: middle;
float: none;
text-align: justify;
}
</style>
<div>
<div class="row">
<div class="col-sm-12 col-lg-12">
<div class="reproblocktitle">
<rtitle>A computational framework for integrative metagenomic and metatranscriptomic analyses</rtitle>
<hr></hr>
<rdoi>DOI: [ <a href="">doi:10.10.1038/nphys1170</a>) ]</rdoi>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-globe" aria-hidden="true"></span><rtitle>Website</rtitle></h4>
<hr></hr>
<rbody>The <b>IMP</b> website hosted within <b>R3lab</b> frame is available <a href="http://r3lab.uni.lu/web/imp/index.html">
here</a>.
</rbody>
</div>
</div>
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-duplicate" aria-hidden="true"></span><rtitle>Source code</rtitle></h4>
<hr></hr>
<rbody>The source code is available on the <a href="https://git-r3lab.uni.lu/shaman.narayanasamy/IMP">LCSB Gitlab</a> where you can traceback what have been done by the authors.</rbody>
</div>
</div>
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><rtitle>Workflow</rtitle></h4>
<hr></hr>
<rbody>Snakemake, a reproducible workflow engine that allow us IMP users execute the same workflow for each analysis.
From <a href="http://bioinformatics.oxfordjournals.org/content/28/19/2520">Köster, Johannes and Rahmann,
Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.</a>
</rbody>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-level-up" aria-hidden="true"></span><rtitle>Data repository</rtitle></h4>
<hr></hr>
<rbody>The <b>IMP</b> data repository is hosted on the <a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/">
LCSB webdav storage</a>. You will find some of the tools installed within IMP.
IMP versions are stored under the <b>dist</b> folder.
</rbody>
</div>
</div>
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-th" aria-hidden="true"></span><rtitle>Environment</rtitle></h4>
<hr></hr>
<rbody>All tools dependencies of IMP are frozen inside a docker container.
The files used to build the container can be found on Gitlab and versioned tarballs of the
containers are found under the <a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/dist/">webdav</a>.
</rbody>
</div>
</div>
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-repeat" aria-hidden="true"></span><rtitle>R toolkit</rtitle></h4>
<hr></hr>
<rbody>
We use the <a href="https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html">
checkpoint</a> library to ensure that all of the necessary R packages are installed
with the correct versions.
</rbody>
</div>
</div>
<div class="col-sm-4 col-lg-4">
<div class="reproblock rfixed">
<h4><span class="glyphicon glyphicon-book" aria-hidden="true"></span><rtitle>Report</rtitle></h4>
<hr></hr>
<rbody>
<b>IMP</b> report contains all information needed to reproduce the same workflow, from the version
of <b>IMP</b> used to make the analysis to the configuration file used to start the workflow.
Everything is condensed and organized within an HTML report. Some reports can be found
<a href="https://webdav-r3lab.uni.lu/public/R3lab/IMP/reports/">here</a>.
</rbody>
</div>
</div>
</div>
</div>
---
layout: default
index: /$R3lab
nav: /index$Home,/frozen/index$Frozen pages,/web/index$Websites
theme: paper
title: Frozen projects
---
<div>
<div class="jumbotron">
<p class="lead">
Here you can find project pages that are related to a published scientific paper.
Project pages must link to all components referenced in the paper and is not modified after the release of the paper.
</p>
</div>
<div class="jumbotron">
<h2>Frozen pages</h2>
{% for page in site.pages %}
{% if page.type == 'frozen' %}
{% assign index = page.index | split:"$" %}
<p>
<span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span> <a href="{{index[0]}}">{{index[1]}}</a>
{{page.description}}
{% endif %}
{% endfor %}
</div>
</div>
---
layout: default
index: ../$R3lab
nav: https://git-r3lab.uni.lu$Gitlab,https://webdav-r3lab.uni.lu$File Storage,https://docker-r3lab.uni.lu$Docker
index: /$R3lab
nav: /index$Home,/frozen/index$Frozen pages,/web/index$Websites
theme: paper
---
<div>
<div class="jumbotron">
<h1>Reproducible Research Results</h1>
<div class="row marketing">
<div class="col-lg-6"></div>
</div>
<div class="row marketing">
<div class="col-lg-6"></div>
</div>
</div>
<div class="jumbotron">
<h2>Hosted websites</h2>
{% for project in site.pages %}
{% if project.type == 'project' %}
{% assign index = project.index | split:"$" %}
<h2>Reproducible blocks</h2>
{% for page in site.pages %}
{% if page.type == 'reproducible' %}
{% assign index = page.index | split:"$" %}
<p>
<span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span> <a href="/web/{{index[0]}}">{{index[1]}}</a>
{{project.description}}
{{page.description}}
{% endif %}
{% endfor %}
</div>
<div class="jumbotron">
<h2>Associated services</h2>
<!-- GITLAB -->
<div class="media">
<div class="media-left">
<a href="https://git-r3lab.uni.lu">
<svg class="media-object" width="80px" height="80px" viewBox="0 0 210 210" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" id="tanuki-logo" style="width:123px">
<g id="Page-1" stroke="none" stroke-width="1" fill="none" fill-rule="evenodd" sketch:type="MSPage">
<g id="logo" sketch:type="MSLayerGroup" transform="translate(0.000000, 10.000000)">
<g id="Page-1" sketch:type="MSShapeGroup">
<g id="Fill-1-+-Group-24">
<g id="Group-24">
<g id="Group">
<path d="M105.0614,193.655 L105.0614,193.655 L143.7014,74.734 L66.4214,74.734 L105.0614,193.655 L105.0614,193.655 Z" id="Fill-4" fill="#E24329" class="tanuki-shape"></path>
<path d="M105.0614,193.6548 L66.4214,74.7338 L12.2684,74.7338 L105.0614,193.6548 L105.0614,193.6548 Z" id="Fill-8" fill="#FC6D26" class="tanuki-shape"></path>
<path d="M12.2685,74.7341 L12.2685,74.7341 L0.5265,110.8731 C-0.5445,114.1691 0.6285,117.7801 3.4325,119.8171 L105.0615,193.6551 L12.2685,74.7341 L12.2685,74.7341 Z" id="Fill-12" fill="#FCA326" class="tanuki-shape"></path>
<path d="M12.2685,74.7342 L66.4215,74.7342 L43.1485,3.1092 C41.9515,-0.5768 36.7375,-0.5758 35.5405,3.1092 L12.2685,74.7342 L12.2685,74.7342 Z" id="Fill-16" fill="#E24329" class="tanuki-shape"></path>
<path d="M105.0614,193.6548 L143.7014,74.7338 L197.8544,74.7338 L105.0614,193.6548 L105.0614,193.6548 Z" id="Fill-18" fill="#FC6D26" class="tanuki-shape"></path>
<path d="M197.8544,74.7341 L197.8544,74.7341 L209.5964,110.8731 C210.6674,114.1691 209.4944,117.7801 206.6904,119.8171 L105.0614,193.6551 L197.8544,74.7341 L197.8544,74.7341 Z" id="Fill-20" fill="#FCA326" class="tanuki-shape"></path>
<path d="M197.8544,74.7342 L143.7014,74.7342 L166.9744,3.1092 C168.1714,-0.5768 173.3854,-0.5758 174.5824,3.1092 L197.8544,74.7342 L197.8544,74.7342 Z" id="Fill-22" fill="#E24329" class="tanuki-shape"></path>
</g>
</g>
</g>
</g>
</g>
</g>
</svg>
</a>
</div>
<div class="media-body">
<h4 class="media-heading">GITLAB</h4>
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec a diam lectus. Sed sit amet ipsum mauris. Maecenas congue ligula ac quam viverra nec consectetur ante hendrerit. Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean ut gravida lorem.
</div>
</div><!-- END GITLAB -->
<br/>
<!-- DOCKER -->
<div class="media">
<div class="media-left">
<a href="https://docker-r3lab.uni.lu">
<img class="media-object" src="img/docker-logo.png" alt="...">
</a>
</div>
<div class="media-body">
<h4 class="media-heading">DOCKER</h4>
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec a diam lectus. Sed sit amet ipsum mauris. Maecenas congue ligula ac quam viverra nec consectetur ante hendrerit. Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean ut gravida lorem.
</div>
</div><!-- END DOCKER -->
<br/>
<!-- WEBDAV -->
<div class="media">
<div class="media-left">
<a href="https://webdav-r3lab.uni.lu">
<img class="media-object" src="img/webdav.png" style="width:123px" />
</a>
</div>
<div class="media-body">
<h4 class="media-heading">WEBDAV</h4>
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec a diam lectus. Sed sit amet ipsum mauris. Maecenas congue ligula ac quam viverra nec consectetur ante hendrerit. Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean ut gravida lorem.
</div>
</div><!-- END WEBDAV -->
</div>
</div>
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