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Commit 43c6b1c4 authored by Jerome Mariette's avatar Jerome Mariette
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add install doc

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docs/example1.html
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......@@ -36,6 +36,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -115,7 +116,6 @@
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/example2.html
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......@@ -35,6 +35,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -91,7 +92,6 @@
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/index.html
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......@@ -35,6 +35,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li class="active"><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -95,7 +96,6 @@
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/jflow-core-component.html
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......@@ -4,7 +4,7 @@
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>jvenn</title>
<title>jflow</title>
<!-- Les styles -->
<link href="css/bootstrap.css" rel="stylesheet" media="screen">
<link href="css/docs.css" rel="stylesheet" media="screen">
......@@ -27,6 +27,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -99,7 +100,6 @@
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/jflow-core-workflow.html
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......@@ -4,7 +4,7 @@
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>jvenn</title>
<title>jflow</title>
<!-- Les styles -->
<link href="css/bootstrap.css" rel="stylesheet" media="screen">
<link href="css/docs.css" rel="stylesheet" media="screen">
......@@ -27,6 +27,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -106,7 +107,6 @@
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/jflow-core.html
View file @ 43c6b1c4
......@@ -4,7 +4,7 @@
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>jvenn</title>
<title>jflow</title>
<!-- Les styles -->
<link href="css/bootstrap.css" rel="stylesheet" media="screen">
<link href="css/docs.css" rel="stylesheet" media="screen">
......@@ -27,6 +27,7 @@
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -51,13 +52,49 @@
<div class="container">
<div class="row">
<div class="span3 bs-docs-sidebar">
<ul class="nav nav-list bs-docs-sidenav affix">
<li class="active"><a href="#introduction"><i class="icon-chevron-right"></i> Introduction</a></li>
<li><a href="#architecture"><i class="icon-chevron-right"></i> Global architecture</a></li>
</ul>
</div>
<div class="span9">
<section id="introduction">
<div class="page-header">
<h1>Introduction</h1>
</div>
<p>Building rich WEB environments aimed at helping scientists analyse their data is a common trend in
bioinformatics. These applications are often specialized WEB portals or generic Workflow management systems
(WMS). The first class provides multiple services and analysis tools in an integrated interface for a specific
experiment or data type. Quite often these systems hide the processing steps in the back-office. The second class,
for example Galaxy, is mainly focused on workflow creation and provides a rather poor end-user interface but enable
to combine tools and data sources as desired. We introduce jflow a fully scalable WMS that can easily be embedded
in any WEB site, providing all WMS features and benefits to your project.</p>
</section>
<section id="architecture">
<div class="page-header">
<h1>Global architecture</h1>
</div>
<p>jflow core is based upon the <a target="_blank" href="http://www.cse.nd.edu/~ccl/software/makeflow/">Makeflow</a>
workflow engine and <a target="_blank" href="https://bitbucket.org/pbui/weaver">weaver</a>, its Python API which is embedded
within jflow. Using makeflow permits to run jflow under different batch systems such as Condor, SGE, Work Queue or a single
multicore machine</p>
<div class="bs-docs-example" style="text-align: center;">
<img width="75%" src="img/jflow-global-architecture.png" class="img-rounded">
</div>
</section>
</div>
</div>
<!-- Footer -->
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
docs/jflow-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">
<link href="css/docs.css" rel="stylesheet" media="screen">
<link href="css/prettify.css" rel="stylesheet" media="screen">
<link href="css/bootstrap-responsive.css" rel="stylesheet" media="screen">
<script type="text/javascript" src="js/jquery.min.js"></script>
<script src="js/bootstrap.min.js"></script>
<script src="js/prettify.js"></script>
</head>
<body data-spy="scroll" data-target=".bs-docs-sidebar">
<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="#">Jflow</a>
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li class="active"><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<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>
</li>
<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>
<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="span3 bs-docs-sidebar">
<ul class="nav nav-list bs-docs-sidenav affix">
<li class="active"><a href="#prerequists"><i class="icon-chevron-right"></i> Prerequists</a></li>
<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>
</div>
<div class="span9">
<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>
</div>
</div>
<hr>
<!-- 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>
</div>
<script>
!function ($) {
$(function(){
window.prettyPrint && prettyPrint()
})
}(window.jQuery)
</script>
</body>
</html>
\ No newline at end of file
docs/jflow-plugin.html
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<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#">
Core
......@@ -112,7 +113,6 @@ $(document).ready(function(){
<footer class="footer">
<div class="container">
<p>Copyright © 2014, INRA | Designed by GenoToul Bioinfo and Sigenae teams.</p>
<p>Code licensed under ....</p>
<ul class="footer-links">
<li><a href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo platform</a></li>
<li class="muted">&middot;</li>
......
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