RAPPEL : Opération de maintenance > ForgeMIA indisponible le 20 Janvier entre 7h et 12h

Commit 55f42a39 authored by Philippe Bardou's avatar Philippe Bardou
Browse files

class=page-header on h1 !

parent 80a02cfc
......@@ -78,15 +78,11 @@
<div class="row">
<div class="col-lg-6">
<div class="page-header">
<h1>Available workflows <small>to run</small></h1>
</div>
<h1 class="page-header">Available workflows <small>to run</small></h1>
<div id="available-workflows-list"></div>
</div>
<div class="col-lg-6">
<div class="page-header">
<h1>Actives workflows <small>to monitor</small></h1>
</div>
<h1 class="page-header">Actives workflows <small>to monitor</small></h1>
<div id="active-workflows-list"></div>
</div>
</div>
......
......@@ -93,9 +93,7 @@
<div class="col-xs-12 col-sm-9">
<section id="component-architecture" class="group">
<div class="page-header">
<h1>Where to add a new component</h1>
</div>
<h1 class="page-header">Where to add a new component</h1>
<p>New component must be added in the general <code>components</code> directory or in a specific
<code>components</code> directory of a workflow. The definition of the component must be
written in <code>myComponentName.py</code> file.</p>
......@@ -119,9 +117,7 @@
</section>
<section id="component" class="group">
<div class="page-header">
<h1>The <i>Component</i> definition</h1>
</div>
<h1 class="page-header">The <i>Component</i> definition</h1>
<p>The new component is a class defined in <code>myComponentName.py</code>. In order to add component you must: </p>
<ul>
<li>Inherit from the <code>Component</code> class</li>
......@@ -149,9 +145,7 @@ class BWAAln (Component):
</section>
<section id="define_parameters" class="group">
<div class="page-header">
<h1>Define parameters</h1>
</div>
<h1 class="page-header">Define parameters</h1>
<p>
The define parameters function is used to add workflow inputs and outputs. Several methods are available to add different
types of parameters. The added parameter will be available as an object attibut, thus be accessible using <code>self.param_name</code>.
......@@ -292,15 +286,11 @@ class BWAAln (Component):
</section>
<section id="process" class="group">
<div class="page-header">
<h1>Overloading <i>process</i></h1>
</div>
<h1 class="page-header">Overloading <i>process</i></h1>
</section>
<section id="other_methods" class="group">
<div class="page-header">
<h1>Other available methods</h1>
</div>
<h1 class="page-header">Other available methods</h1>
<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>
......
......@@ -84,9 +84,7 @@
<div class="col-xs-12 col-sm-9">
<section id="workflow-architecture" class="group">
<div class="page-header">
<h1>Where to add a new workflow</h1>
</div>
<h1 class="page-header">Where to add a new workflow</h1>
<p>The new wokflow must be added as a new python package in the <code>workflows</code> package. The definition of
the workflows must be written in <code><a href="#workflow">__init__.py</a></code>.</p>
<p>User can optionaly add : </p>
......@@ -116,9 +114,7 @@
</section>
<section id="workflow" class="group">
<div class="page-header">
<h1>The <i>Workflow</i> definition</h1>
</div>
<h1 class="page-header">The <i>Workflow</i> definition</h1>
<p>The new workflow is a class defined in <code>__init__.py</code>. In order to add workflow you must: </p>
<ul>
......@@ -161,9 +157,7 @@ class Alignment (Workflow):
</section>
<section id="define_parameters" class="group">
<div class="page-header">
<h1>Define parameters</h1>
</div>
<h1 class="page-header">Define parameters</h1>
<p>
The define parameters function is used to add workflow inputs and outputs. Several methods are available to add different
types of parameters. The added parameter will be available as an object attibut, thus be accessible using <code>self.param_name</code>.
......@@ -561,9 +555,7 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
</section>
<section id="process" class="group">
<div class="page-header">
<h1>Overloading <i>process</i></h1>
</div>
<h1 class="page-header">Overloading <i>process</i></h1>
<p>The <code>process()</code> method defines the actions done by the workflow.</p>
<p>In process you can add components with the method <code>add_component()</code>.
A component is class which represents a step in the workflow defined by a set of commands.
......@@ -628,9 +620,7 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
</section>
<section id="other_methods" class="group">
<div class="page-header">
<h1>Other available methods</h1>
</div>
<h1 class="page-header">Other available methods</h1>
<div id="pre_process" class="subgroup">
<h2>Overloading <i>pre process</i></h2>
<p>This method is executed brefore process and cannot be used to add components.</p>
......
......@@ -74,9 +74,7 @@
<div class="col-xs-12 col-sm-9">
<section id="introduction" class="group">
<div class="page-header">
<h1>Introduction</h1>
</div>
<h1 class="page-header">Introduction</h1>
<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
......@@ -87,9 +85,7 @@
</section>
<section id="architecture" class="group">
<div class="page-header">
<h1>Global architecture</h1>
</div>
<h1 class="page-header">Global architecture</h1>
<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
......
......@@ -74,9 +74,7 @@
<div class="col-xs-12 col-sm-9">
<section id="prerequists">
<div class="page-header">
<h1>Prerequists</h1>
</div>
<h1 class="page-header">Prerequists</h1>
<ul>
<li><a target="_blank" href="https://www.python.org/">Python</a>: the supported versions are 2.7 or higher. Modules required :
<ul>
......@@ -89,25 +87,19 @@
</section>
<section id="downloadl">
<div class="page-header">
<h1>Download the latest copy</h1>
</div>
<h1 class="page-header">Download the latest copy</h1>
<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>
<h1 class="page-header">Extract the archive</h1>
<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>
<h1 class="page-header">Configure the application</h1>
<pre class="prettyprint linenums">
[global]
# uncomment and set if not in the PATH, should be version >= 4.2.2
......@@ -145,9 +137,7 @@ tmp_directory = /path/to/tmp
</section>
<section id="test">
<div class="page-header">
<h1>Test your installation</h1>
</div>
<h1 class="page-header">Test your installation</h1>
<p>The application embed 1 WEB site example, enter the following command lines to run the WEB server:</p>
<pre class="prettyprint linenums">
[user@hostname:~] python bin/jflow_server.py --daemon</pre>
......
......@@ -444,7 +444,6 @@
</section>
<section id="wfstatus">
<h1 class="page-header">Workflow status <small>wfstatus()</small></h1>
<div id="wfstatus_example" class="subgroup">
......
......@@ -128,7 +128,6 @@
<section id="second_step" class="group">
<h1 class="page-header">2nd step <small>create required components</small></h1>
<div id="BWAIndex_component" class="subgroup">
<h2>BWAIndex component</h2>
<p></p>
......
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