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Commit dbf0360a authored by Jerome Mariette's avatar Jerome Mariette
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first doc for nG6

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docs/css/ladda-themeless.min.css 0 → 100644
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/*
* Ladda
* http://lab.hakim.se/ladda
* MIT licensed
*
* Copyright (C) 2013 Hakim El Hattab, http://hakim.se
*/.ladda-button{position:relative}.ladda-button .ladda-spinner{position:absolute;z-index:2;display:inline-block;width:32px;height:32px;top:50%;margin-top:-16px;opacity:0;pointer-events:none}.ladda-button .ladda-label{position:relative;z-index:3}.ladda-button .ladda-progress{position:absolute;width:0;height:100%;left:0;top:0;background:rgba(0,0,0,0.2);visibility:hidden;opacity:0;-webkit-transition:0.1s linear all !important;-moz-transition:0.1s linear all !important;-ms-transition:0.1s linear all !important;-o-transition:0.1s linear all !important;transition:0.1s linear all !important}.ladda-button[data-loading] .ladda-progress{opacity:1;visibility:visible}.ladda-button,.ladda-button .ladda-spinner,.ladda-button .ladda-label{-webkit-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-moz-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-ms-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-o-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important}.ladda-button[data-style=zoom-in],.ladda-button[data-style=zoom-in] .ladda-spinner,.ladda-button[data-style=zoom-in] .ladda-label,.ladda-button[data-style=zoom-out],.ladda-button[data-style=zoom-out] .ladda-spinner,.ladda-button[data-style=zoom-out] .ladda-label{-webkit-transition:0.3s ease all !important;-moz-transition:0.3s ease all !important;-ms-transition:0.3s ease all !important;-o-transition:0.3s ease all !important;transition:0.3s ease all !important}.ladda-button[data-style=expand-right] .ladda-spinner{right:14px}.ladda-button[data-style=expand-right][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-right][data-size="xs"] .ladda-spinner{right:4px}.ladda-button[data-style=expand-right][data-loading]{padding-right:56px}.ladda-button[data-style=expand-right][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=expand-right][data-loading][data-size="s"],.ladda-button[data-style=expand-right][data-loading][data-size="xs"]{padding-right:40px}.ladda-button[data-style=expand-left] .ladda-spinner{left:14px}.ladda-button[data-style=expand-left][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-left][data-size="xs"] .ladda-spinner{left:4px}.ladda-button[data-style=expand-left][data-loading]{padding-left:56px}.ladda-button[data-style=expand-left][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=expand-left][data-loading][data-size="s"],.ladda-button[data-style=expand-left][data-loading][data-size="xs"]{padding-left:40px}.ladda-button[data-style=expand-up]{overflow:hidden}.ladda-button[data-style=expand-up] .ladda-spinner{top:-32px;left:50%;margin-left:-16px}.ladda-button[data-style=expand-up][data-loading]{padding-top:54px}.ladda-button[data-style=expand-up][data-loading] .ladda-spinner{opacity:1;top:14px;margin-top:0}.ladda-button[data-style=expand-up][data-loading][data-size="s"],.ladda-button[data-style=expand-up][data-loading][data-size="xs"]{padding-top:32px}.ladda-button[data-style=expand-up][data-loading][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-up][data-loading][data-size="xs"] .ladda-spinner{top:4px}.ladda-button[data-style=expand-down]{overflow:hidden}.ladda-button[data-style=expand-down] .ladda-spinner{top:62px;left:50%;margin-left:-16px}.ladda-button[data-style=expand-down][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-down][data-size="xs"] .ladda-spinner{top:40px}.ladda-button[data-style=expand-down][data-loading]{padding-bottom:54px}.ladda-button[data-style=expand-down][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=expand-down][data-loading][data-size="s"],.ladda-button[data-style=expand-down][data-loading][data-size="xs"]{padding-bottom:32px}.ladda-button[data-style=slide-left]{overflow:hidden}.ladda-button[data-style=slide-left] .ladda-label{position:relative}.ladda-button[data-style=slide-left] .ladda-spinner{left:100%;margin-left:-16px}.ladda-button[data-style=slide-left][data-loading] .ladda-label{opacity:0;left:-100%}.ladda-button[data-style=slide-left][data-loading] .ladda-spinner{opacity:1;left:50%}.ladda-button[data-style=slide-right]{overflow:hidden}.ladda-button[data-style=slide-right] .ladda-label{position:relative}.ladda-button[data-style=slide-right] .ladda-spinner{right:100%;margin-left:-16px}.ladda-button[data-style=slide-right][data-loading] .ladda-label{opacity:0;left:100%}.ladda-button[data-style=slide-right][data-loading] 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.ladda-label{position:relative;display:inline-block}.ladda-button[data-style=zoom-in][data-loading] .ladda-label{opacity:0;-webkit-transform:scale(2.2);-moz-transform:scale(2.2);-ms-transform:scale(2.2);-o-transform:scale(2.2);transform:scale(2.2)}.ladda-button[data-style=zoom-in][data-loading] .ladda-spinner{opacity:1;-webkit-transform:none;-moz-transform:none;-ms-transform:none;-o-transform:none;transform:none}.ladda-button[data-style=contract]{overflow:hidden;width:100px}.ladda-button[data-style=contract] .ladda-spinner{left:50%;margin-left:-16px}.ladda-button[data-style=contract][data-loading]{border-radius:50%;width:52px}.ladda-button[data-style=contract][data-loading] .ladda-label{opacity:0}.ladda-button[data-style=contract][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=contract-overlay]{overflow:hidden;width:100px;box-shadow:0px 0px 0px 3000px rgba(0,0,0,0)}.ladda-button[data-style=contract-overlay] .ladda-spinner{left:50%;margin-left:-16px}.ladda-button[data-style=contract-overlay][data-loading]{border-radius:50%;width:52px;box-shadow:0px 0px 0px 3000px rgba(0,0,0,0.8)}.ladda-button[data-style=contract-overlay][data-loading] .ladda-label{opacity:0}.ladda-button[data-style=contract-overlay][data-loading] .ladda-spinner{opacity:1}
docs/css/ladda.min.css 0 → 100644
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/*
* Ladda
* http://lab.hakim.se/ladda
* MIT licensed
*
* Copyright (C) 2013 Hakim El Hattab, http://hakim.se
*/.ladda-button{position:relative}.ladda-button .ladda-spinner{position:absolute;z-index:2;display:inline-block;width:32px;height:32px;top:50%;margin-top:-16px;opacity:0;pointer-events:none}.ladda-button .ladda-label{position:relative;z-index:3}.ladda-button .ladda-progress{position:absolute;width:0;height:100%;left:0;top:0;background:rgba(0,0,0,0.2);visibility:hidden;opacity:0;-webkit-transition:0.1s linear all !important;-moz-transition:0.1s linear all !important;-ms-transition:0.1s linear all !important;-o-transition:0.1s linear all !important;transition:0.1s linear all !important}.ladda-button[data-loading] .ladda-progress{opacity:1;visibility:visible}.ladda-button,.ladda-button .ladda-spinner,.ladda-button .ladda-label{-webkit-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-moz-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-ms-transition:0.3s cubic-bezier(0.175, 0.885, 0.32, 1.275) all !important;-o-transition:0.3s 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.ladda-spinner{opacity:1}.ladda-button[data-style=expand-right][data-loading][data-size="s"],.ladda-button[data-style=expand-right][data-loading][data-size="xs"]{padding-right:40px}.ladda-button[data-style=expand-left] .ladda-spinner{left:14px}.ladda-button[data-style=expand-left][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-left][data-size="xs"] .ladda-spinner{left:4px}.ladda-button[data-style=expand-left][data-loading]{padding-left:56px}.ladda-button[data-style=expand-left][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=expand-left][data-loading][data-size="s"],.ladda-button[data-style=expand-left][data-loading][data-size="xs"]{padding-left:40px}.ladda-button[data-style=expand-up]{overflow:hidden}.ladda-button[data-style=expand-up] .ladda-spinner{top:-32px;left:50%;margin-left:-16px}.ladda-button[data-style=expand-up][data-loading]{padding-top:54px}.ladda-button[data-style=expand-up][data-loading] .ladda-spinner{opacity:1;top:14px;margin-top:0}.ladda-button[data-style=expand-up][data-loading][data-size="s"],.ladda-button[data-style=expand-up][data-loading][data-size="xs"]{padding-top:32px}.ladda-button[data-style=expand-up][data-loading][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-up][data-loading][data-size="xs"] .ladda-spinner{top:4px}.ladda-button[data-style=expand-down]{overflow:hidden}.ladda-button[data-style=expand-down] .ladda-spinner{top:62px;left:50%;margin-left:-16px}.ladda-button[data-style=expand-down][data-size="s"] .ladda-spinner,.ladda-button[data-style=expand-down][data-size="xs"] .ladda-spinner{top:40px}.ladda-button[data-style=expand-down][data-loading]{padding-bottom:54px}.ladda-button[data-style=expand-down][data-loading] .ladda-spinner{opacity:1}.ladda-button[data-style=expand-down][data-loading][data-size="s"],.ladda-button[data-style=expand-down][data-loading][data-size="xs"]{padding-bottom:32px}.ladda-button[data-style=slide-left]{overflow:hidden}.ladda-button[data-style=slide-left] .ladda-label{position:relative}.ladda-button[data-style=slide-left] .ladda-spinner{left:100%;margin-left:-16px}.ladda-button[data-style=slide-left][data-loading] .ladda-label{opacity:0;left:-100%}.ladda-button[data-style=slide-left][data-loading] .ladda-spinner{opacity:1;left:50%}.ladda-button[data-style=slide-right]{overflow:hidden}.ladda-button[data-style=slide-right] .ladda-label{position:relative}.ladda-button[data-style=slide-right] .ladda-spinner{right:100%;margin-left:-16px}.ladda-button[data-style=slide-right][data-loading] .ladda-label{opacity:0;left:100%}.ladda-button[data-style=slide-right][data-loading] .ladda-spinner{opacity:1;left:50%}.ladda-button[data-style=slide-up]{overflow:hidden}.ladda-button[data-style=slide-up] .ladda-label{position:relative}.ladda-button[data-style=slide-up] .ladda-spinner{left:50%;margin-left:-16px;margin-top:1em}.ladda-button[data-style=slide-up][data-loading] .ladda-label{opacity:0;top:-1em}.ladda-button[data-style=slide-up][data-loading] .ladda-spinner{opacity:1;margin-top:-16px}.ladda-button[data-style=slide-down]{overflow:hidden}.ladda-button[data-style=slide-down] .ladda-label{position:relative}.ladda-button[data-style=slide-down] .ladda-spinner{left:50%;margin-left:-16px;margin-top:-2em}.ladda-button[data-style=slide-down][data-loading] .ladda-label{opacity:0;top:1em}.ladda-button[data-style=slide-down][data-loading] .ladda-spinner{opacity:1;margin-top:-16px}.ladda-button[data-style=zoom-out]{overflow:hidden}.ladda-button[data-style=zoom-out] 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8px}.ladda-button[data-size=xs] .ladda-label{font-size:0.7em}.ladda-button[data-size=s]{padding:6px 10px}.ladda-button[data-size=s] .ladda-label{font-size:0.9em}.ladda-button[data-size=l] .ladda-label{font-size:1.2em}.ladda-button[data-size=xl] .ladda-label{font-size:1.5em}
docs/css/prettify.css 0 → 100644
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.com { color: #93a1a1; }
.lit { color: #195f91; }
.pun, .opn, .clo { color: #93a1a1; }
.fun { color: #dc322f; }
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-webkit-box-shadow: inset 40px 0 0 #fbfbfc, inset 41px 0 0 #ececf0;
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line-height: 20px;
text-shadow: 0 1px 0 #fff;
}
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docs/index.html 0 → 100644
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>nG6</title>
<!-- Le styles -->
<link href="css/bootstrap.css" rel="stylesheet">
<style type="text/css">
body {
padding-top: 60px;
padding-bottom: 40px;
}
</style>
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link rel="shortcut icon" href="../assets/ico/favicon.png">
<link href="css/docs.css" rel="stylesheet">
<link href="js/google-code-prettify/prettify.css" rel="stylesheet">
</head>
<body>
<div class="navbar navbar-inverse navbar-fixed-top">
<div class="navbar-inner">
<div class="container">
<button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="brand" href="#">nG6</a>
<div class="nav-collapse collapse">
<ul class="nav">
<li class="active"><a href="./index.html">About</a></li>
<li><a href="./install.html">Install</a></li>
<li><a target="_blank" href="https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ng6/index.php/Accueil">Sources</a></li>
<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
</div>
<!-- Subhead ================================================== -->
<header class="jumbotron subhead" id="overview">
<div class="container">
<h1>nG6</h1>
<p class="lead">
Next Generation Sequencing Information System.
</p>
</div>
</header>
<div class="container">
<div class="marketing">
<p class="marketing-byline"></p>
<div class="row">
<div class="span6">
<h2>Add new analysis</h2>
<p>Your workflow requires new analysis, learn how to add new ones.</p>
</div>
<div class="span6">
<h2>Add new workflows</h2>
<p>Learn how to add new workflows.</p>
</div>
</div>
</div>
</div> <!-- /container -->
<!-- Footer -->
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
<li><a href="http://www.sigenae.org/" target="_blank">Sigenae platform</a></li>
<li class="muted">&middot;</li>
<li><a href="http://www.international.inra.fr/" target="_blank">INRA</a></li>
</ul>
</div>
</footer>
<!-- Le javascript
================================================== -->
<script type="text/javascript" src="js/jquery.min.js"></script>
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<script src="js/prettify.js"></script>
</body>
</html>
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docs/install.html 0 → 100644
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<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>jflow</title>
<!-- Les styles -->
<link href="css/bootstrap.css" rel="stylesheet" media="screen">
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<a class="brand" href="#">Jflow</a>
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<li><a href="./index.html">About</a></li>
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Core
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<li> <a href="./jflow-core.html">Jflow overview</a> </li>
<li> <a href="./jflow-core-component.html">Adding component</a> </li>
<li> <a href="./jflow-core-workflow.html">Adding workflow</a> </li>
</ul>
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<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example 1</a></li>
<li><a href="./example2.html">Example 2</a></li>
<li><a target="_blank" href="https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/jflow/index.php/Accueil">Sources</a></li>
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<li><a href="#downloadl"><i class="icon-chevron-right"></i> Download the latest copy</a></li>
<li><a href="#extract"><i class="icon-chevron-right"></i> Extract the archive</a></li>
<li><a href="#configure"><i class="icon-chevron-right"></i> Configure the application</a></li>
<li><a href="#test"><i class="icon-chevron-right"></i> Test your installation</a></li>
</ul>
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<section id="prerequists">
<div class="page-header">
<h1>Prerequists</h1>
</div>
<ul>
<li><a target="_blank" href="https://www.python.org/">Python</a>: the supported versions are 2.7 or higher. Modules required :
<ul>
<li><a target="_blank" href="http://www.cherrypy.org/">Cherrypy</a>: A Minimalist Python Web Framework.</li>
</ul>
</li>
<li><a target="_blank" href="http://www.cse.nd.edu/~ccl/software/makeflow/">Makeflow v3.7.3</a>: a workflow
engine for executing large complex workflows on clusters, clouds, and grids. (makeflow v4.0.2 version introduces
a bug that will be corrected in next release) </li>
</ul>
</section>
<section id="downloadl">
<div class="page-header">
<h1>Download the latest copy</h1>
</div>
<p>The latest version can be downloaded from the <a href="https://mulcyber.toulouse.inra.fr/frs/?group_id=186" target="_blank">download page</a>.</p>
</section>
<section id="extract">
<div class="page-header">
<h1>Extract the archive</h1>
</div>
<pre class="prettyprint linenums">
[user@hostname:~] tar xzvf jflow_v1.0.tar.gz
[user@hostname:~] cd jflow_v1.0</pre>
</section>
<section id="configure">
<div class="page-header">
<h1>Configure the application</h1>
</div>
<pre class="prettyprint linenums">
[global]
# uncomment and set if not in the PATH
#makeflow = /usr/bin/makeflow
# batch system type: local, condor, sge, moab, cluster, wq, hadoop, mpi-queue
batch_system_type = local
# add these options to all batch submit files
batch_options =
# add these options to limit the number of jobs sumitted in parallel
limit_submission = 100
# on which socket host should run the web server
server_socket_host = 127.0.0.1
# on which socket port should run the web server
server_socket_port = 8080
[storage]
# where should be written the log file
log_file = /path/to/jflow.log
# Where should the pipelines write results, should be accessible
# by all cluster nodes
work_directory = /path/to/work
# Where should the pipelines write temporary files, should be
# accessible by all cluster nodes
tmp_directory = /path/to/tmp
[softwares]
# uncomment and set if not in the PATH
#blastall = /usr/bin/blastall
#formatdb = /usr/bin/formatdb
#sfffile = /usr/bin/sfffile
#fastqc = /usr/bin/fastqc
#runAssembly = /usr/bin/runAssembly
#bwa = /usr/bin/bwa
#samtools = /usr/bin/samtools</pre>
</section>
<section id="test">
<div class="page-header">
<h1>Test your installation</h1>
</div>
<p>The application embed 2 WEB site examples, enter the following command lines to run the WEB server:</p>
<pre class="prettyprint linenums">
[user@hostname:~] python bin/jflow_server.py --daemon</pre>
<p>And go on the <a href="./example1.html">Example 1</a> or <a href="./example2.html">Example 2</a> WEB pages.
You should have the following display with the alignment workflow available and no actives workflows.</p>
<div class="bs-docs-example" style="text-align: center;">
<img width="75%" src="img/jflow-test.png" class="img-rounded">
</div>
</section>
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