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Commit 65a3ee07 authored by Philippe Bardou's avatar Philippe Bardou
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Doc draft

parent d12e4f2e
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docs/css/theme.css
View file @ 65a3ee07
body {
padding-top: 70px;
padding-top: 50px;
padding-bottom: 30px;
}
......@@ -25,9 +25,7 @@ html,
body {
overflow-x: hidden; /* Prevent scroll on narrow devices */
}
body {
padding-top: 70px;
}
footer {
padding: 30px 0;
}
......@@ -76,3 +74,87 @@ footer {
width: 50%; /* 6 columns */
}
}
.fixed {
position: fixed;
}
/* sidebar */
.bs-docs-sidebar {
padding-left: 20px;
margin-top: 20px;
margin-bottom: 20px;
}
}.bs-docs-sidenav {
margin-top: 20px;
margin-bottom: 20px;
}
.bs-docs-sidebar .nav>li>a {
display: block;
padding: 4px 20px;
font-size: 13px;
font-weight: 500;
color: #767676;
}
.bs-docs-sidebar .nav>li>a:focus, .bs-docs-sidebar .nav>li>a:hover {
padding-left: 19px;
color: #428bca;
text-decoration: none;
background-color: transparent;
border-left: 1px solid #428bca;
}
.bs-docs-sidebar .nav>.active:focus>a, .bs-docs-sidebar .nav>.active:hover>a, .bs-docs-sidebar .nav>.active>a {
padding-left: 18px;
font-weight: 700;
color: #428bca;
background-color: transparent;
border-left: 2px solid #428bca;
}
.bs-docs-sidebar .nav .nav {
display: none;
padding-bottom: 10px;
}
.bs-docs-sidebar .nav .nav>li>a {
padding-top: 1px;
padding-bottom: 1px;
padding-left: 30px;
font-size: 12px;
font-weight: 400;
}
.bs-docs-sidebar .nav .nav>li>a:focus,
.bs-docs-sidebar .nav .nav>li>a:hover {
padding-left: 29px;
}
.bs-docs-sidebar .nav .nav>.active:focus>a,
.bs-docs-sidebar .nav .nav>.active:hover>a,
.bs-docs-sidebar .nav .nav>.active>a {
padding-left: 28px;
font-weight: 500;
}
/* hide inactive nested list */
.bs-docs-sidebar .nav ul.nav {
display: none;
}
/* show active nested list */
.bs-docs-sidebar .nav>.active>ul.nav {
display: block;
}
.group, .subgroup {
padding-top: 50px;
margin-top: -50px;
}
/* pre highlight */
.pre-hl {
word-break: normal;
word-wrap: normal;
}
/* pre code highlight */
.pre-hl code {
white-space: inherit;
font-weight: bold;
}
\ No newline at end of file
docs/css/tomorrow-night-eighties.css 0 → 100644
View file @ 65a3ee07
/* Tomorrow Night Eighties Theme */
/* Original theme - https://github.com/chriskempson/tomorrow-theme */
/* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
/* Tomorrow Comment */
.hljs-comment {
color: #999999;
}
/* Tomorrow Red */
.hljs-variable,
.hljs-attribute,
.hljs-tag,
.hljs-regexp,
.ruby .hljs-constant,
.xml .hljs-tag .hljs-title,
.xml .hljs-pi,
.xml .hljs-doctype,
.html .hljs-doctype,
.css .hljs-id,
.css .hljs-class,
.css .hljs-pseudo {
color: #f2777a;
}
/* Tomorrow Orange */
.hljs-number,
.hljs-preprocessor,
.hljs-pragma,
.hljs-built_in,
.hljs-literal,
.hljs-params,
.hljs-constant {
color: #f99157;
}
/* Tomorrow Yellow */
.ruby .hljs-class .hljs-title,
.css .hljs-rules .hljs-attribute {
color: #ffcc66;
}
/* Tomorrow Green */
.hljs-string,
.hljs-value,
.hljs-inheritance,
.hljs-header,
.ruby .hljs-symbol,
.xml .hljs-cdata {
color: #99cc99;
}
/* Tomorrow Aqua */
.hljs-title,
.css .hljs-hexcolor {
color: #66cccc;
}
/* Tomorrow Blue */
.hljs-function,
.python .hljs-decorator,
.python .hljs-title,
.ruby .hljs-function .hljs-title,
.ruby .hljs-title .hljs-keyword,
.perl .hljs-sub,
.javascript .hljs-title,
.coffeescript .hljs-title {
color: #6699cc;
}
/* Tomorrow Purple */
.hljs-keyword,
.javascript .hljs-function {
color: #cc99cc;
}
.hljs {
display: block;
overflow-x: auto;
background: #2d2d2d;
color: #cccccc;
padding: 0.5em;
-webkit-text-size-adjust: none;
}
.coffeescript .javascript,
.javascript .xml,
.tex .hljs-formula,
.xml .javascript,
.xml .vbscript,
.xml .css,
.xml .hljs-cdata {
opacity: 0.5;
}
docs/example1.html
View file @ 65a3ee07
......@@ -41,21 +41,20 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="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>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li class="active"><a href="./example1.html">Example</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>
......@@ -132,7 +131,7 @@
<hr>
<footer>
<div class="container" style="text-align: center;">
<p>Copyright © 2014, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
<p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
</div>
</footer>
......
docs/index.html
View file @ 65a3ee07
......@@ -34,21 +34,24 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li class="active"><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="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-architecture">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type">Adding data type</a></li>
<li><a href="./jflow-format">Adding file format</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example</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>
......@@ -68,27 +71,42 @@
<!-- Example row of columns -->
<div class="row">
<div class="col-lg-4">
<h2>Customize jflow</h2>
<div class="col-lg-3">
<h3>Plugin insertion</h3>
<p>Learn how to insert the jflow plugin within your own application.</p>
<p><a class="btn btn-primary" href="./jflow-plugin.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-4">
<h2>Add new components</h2>
<div class="col-lg-3">
<h3>Add new workflows</h3>
<p>Learn how to add new workflows.</p>
</div>
<div class="col-lg-3">
<h3>Add new components</h3>
<p>Your workflow requires new component, learn how to add new ones.</p>
<p><a class="btn btn-primary" href="./jflow-core-component.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-4">
<h2>Add new workflows</h2>
<p>Learn how to add new workflows.</p>
<div class="col-lg-3">
<h3>Example</h3>
<p>Check out an example of jflow integration.</p>
</div>
</div>
<div class="row">
<div class="col-lg-3">
<p><a class="btn btn-primary" href="./jflow-plugin.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-3">
<p><a class="btn btn-primary" href="./jflow-core-workflow.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-3">
<p><a class="btn btn-primary" href="./jflow-core-component.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-3">
<p><a class="btn btn-primary" href="./example1.html" role="button">View details &raquo;</a></p>
</div>
</div>
<hr>
<footer>
<div class="container" style="text-align: center;">
<p>Copyright © 2014, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
<p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
</div>
</footer>
......
docs/jflow-core-component.html
View file @ 65a3ee07
......@@ -33,21 +33,20 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="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>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example</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>
......@@ -57,18 +56,17 @@
</div>
<div class="container">
<div class="row row-offcanvas row-offcanvas-right">
<div class="col-xs-6 col-sm-3 sidebar-offcanvas" id="sidebar" role="navigation">
<div class="list-group">
<a href="#component" class="list-group-item active">Component</a>
<a href="#define_parameters" class="list-group-item">Define_parameters</a>
<a href="#process" class="list-group-item">Process</a>
<a href="#other_methods" class="list-group-item">Other methods</a>
<a href="#where" class="list-group-item">Where adding the class</a>
</div>
</div>
<div class="row">
<!--Nav Bar -->
<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#component" class="active">Component</a></li>
<li><a href="#define_parameters">Define_parameters</a></li>
<li><a href="#process">Process</a></li>
<li><a href="#other_methods">Other methods</a></li>
<li><a href="#where">Where adding the class</a></li>
</ul>
</nav>
<div class="col-xs-12 col-sm-9">
<p class="pull-right visible-xs">
......@@ -111,7 +109,7 @@
<hr>
<footer>
<div class="container" style="text-align: center;">
<p>Copyright © 2014, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
<p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
</div>
</footer>
......@@ -126,6 +124,11 @@
<!-- IE10 viewport hack for Surface/desktop Windows 8 bug -->
<!-- <script src="../../assets/js/ie10-viewport-bug-workaround.js"></script> -->
<script src="js/offcanvas.js"></script>
<script type='text/javascript'>
$('body').scrollspy({
target: '.bs-docs-sidebar',
offset: 150
});
</script>
</body>
</html>
\ No newline at end of file
docs/jflow-core-workflow.html
View file @ 65a3ee07
......@@ -14,6 +14,9 @@
<!-- Custom styles for this template -->
<link href="css/theme.css" rel="stylesheet">
<!-- Highlight code -->
<link href="css/tomorrow-night-eighties.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
......@@ -33,21 +36,20 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="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>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example</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>
......@@ -57,55 +59,102 @@
</div>
<div class="container">
<div class="row row-offcanvas row-offcanvas-right">
<div class="col-xs-6 col-sm-3 sidebar-offcanvas" id="sidebar" role="navigation">
<div class="list-group">
<a href="#workflow" class="list-group-item active">Workflow</a>
<a href="#pre_process" class="list-group-item">Pre process</a>
<a href="#process" class="list-group-item">Process</a>
<a href="#post_process" class="list-group-item">Post pocess</a>
<a href="#other_methods" class="list-group-item">Other methods</a>
<a href="#where" class="list-group-item">Where adding the class</a>
</div>
</div>
<!--Nav Bar -->
<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#workflow" class="active">Adding workflow</a></li>
<li><a href="#define_parameters">Define parameters</a>
<ul class="nav nav-stacked">
<li><a href="#add_parameter">Add parameter</a></li>
<li><a href="#add_parameter_list">Add parameter list</a></li>
<li><a href="#add_input_directory">Add input directory</a></li>
<li><a href="#add_input_file">Add input file</a></li>
<li><a href="#add_input_file_list">Add input file list</a></li>
<li><a href="#add_multiple_parameter">Add multiple parameter</a></li>
<li><a href="#add_multiple_parameter_list">Add multiple parameter list</a></li>
<li><a href="#add_exclusion_rule">Add exclusion rule</a></li>
</ul>
</li>
<li><a href="#process">Process</a></li>
<li><a href="#other_methods">Other methods</a>
<ul class="nav nav-stacked">
<li><a href="#pre_process">Pre process</a></li>
<li><a href="#post_process">Post process</a></li>
</ul>
</li>
<li><a href="#where">Where adding the class</a></li>
</ul>
</nav>
<div class="col-xs-12 col-sm-9">
<p class="pull-right visible-xs">
<button type="button" class="btn btn-primary btn-xs" data-toggle="offcanvas">Toggle nav</button>
</p>
<section id="workflow">
<section id="workflow" class="group">
<div class="page-header">
<h1>The <i>Workflow</i> class</h1>
</div>
</section>
<section id="pre_process">
<div class="page-header">
<h1>Overloading <i>pre_process</i></h1>
In order to add workflow you must:
<ul>
<li>Inherit from the <i>Workflow</i> class</li>
<li>Implement the <b>get_description()</b> function to define the workflow description</li>
<li>Implement the <b>define_parameters()</b> function to add the workflow inputs and parameters</li>
<li>Implement the <b>process()</b> function by adding components and provide the component arguments</li>
<li>Link components inputs and outputs (typing test is done)</li>
</ul>
<div>
<pre class="pre-hl "><code class="python">from jflow.workflow import Workflow
from jflow.parameter import InputFileList, InputFile
class Alignment (Workflow):
def get_description(self):
return "Align reads against a reference genome"
def define_parameters(self, function="process"):
self.add_input_file_list("read_1", "Which read1 should be used", file_format="fastq", required=True)
self.add_input_file_list("read_2", "Which read2 should be used", file_format="fastq")
self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, file_format="fasta")
def process(self):
"""
Run the workflow
"""
# index the reference genome
bwaindex = self.add_component("BWAIndex", [self.refernce_genome])
# align reads against indexed genome
bwa = self.add_component("BWA", [bwaindex.databank, self.read_1, self.read_2])
</code></pre>
</div>
</section>
<section id="process">
<section id="define_parameters" class="group">
<div class="page-header">
<h1>Overloading <i>process</i></h1>
<h1>Define parameters</h1>
</div>
<div id="add_parameter" class="subgroup"><h2>Add parameter</h2></div>
<div id="add_parameter_list" class="subgroup"><h2>Add parameter list</h2></div>
<div id="add_input_directory" class="subgroup"><h2>Add input directory</h2></div>
<div id="add_input_file" class="subgroup"><h2>Add input file</h2></div>
<div id="add_input_file_list" class="subgroup"><h2>Add input file list</h2></div>
<div id="add_multiple_parameter" class="subgroup"><h2>Add multiple parameter</h2></div>
<div id="add_multiple_parameter_list" class="subgroup"><h2>Add multiple parameter list</h2></div>
<div id="add_exclusion_rule" class="subgroup"><h2>Add exclusion rule</h2></div>
</section>
<section id="post_process">
<section id="process" class="group">
<div class="page-header">
<h1>Overloading <i>post_process</i></h1>
<h1>Overloading <i>process</i></h1>
</div>
</section>
<section id="other_methods">
<section id="other_methods" class="group">
<div class="page-header">
<h1>Other available methods</h1>
</div>
<div id="pre_process" class="subgroup"><h2>Overloading pre process</h2></div>
<div id="post_process" class="subgroup"><h2>Overloading post process</h2></div>
</section>
<section id="where">
<section id="where" class="group">
<div class="page-header">
<h1>Where should the class be added</h1>
</div>
......@@ -116,7 +165,7 @@
<hr>
<footer>
<div class="container" style="text-align: center;">
<p>Copyright © 2014, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
<p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
</div>
</footer>
......@@ -130,7 +179,17 @@
<!-- <script src="../../assets/js/docs.min.js"></script> -->
<!-- IE10 viewport hack for Surface/desktop Windows 8 bug -->
<!-- <script src="../../assets/js/ie10-viewport-bug-workaround.js"></script> -->
<script src="js/offcanvas.js"></script>
<!-- Highlight code -->
<script src="js/highlight.pack.js"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="js/offcanvas.js"></script>
<script type='text/javascript'>
$('body').scrollspy({
target: '.bs-docs-sidebar',
offset: 150
});
</script>
</body>
</html>
\ No newline at end of file
docs/jflow-install.html
View file @ 65a3ee07
......@@ -33,21 +33,20 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li class="active"><a href="./jflow-install.html">Install</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="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>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example</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>
......@@ -57,18 +56,17 @@
</div>