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Commit 06682064 authored by Penom Nom's avatar Penom Nom
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update install documentation

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<ul class="nav">
<li><a href="./index.html">About</a></li>
<li class="active"><a href="./install.html">Install</a></li>
<li><a target="_blank" href="https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/jflow/index.php/Accueil">Sources</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>
</div>
......@@ -51,41 +51,55 @@
<section id="prerequists">
<div class="page-header">
<h1>Prerequists</h1>
<h2>Prerequists</h2>
</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>
<li>argparse</li>
<li>MySQLdb</li>
<li>argparse</li>
<li><a target="_blank" href="http://www.cherrypy.org/">Cherrypy</a> to run the jflow server</li>
<li><a target="_blank" href="http://www.numpy.org/">Numpy</a> used to produce some statistics</li>
</ul>
</li>
<li>an existing <a target="_blank" href="http://www.mysql.fr/">mysql</a> database: the database should be accessible from
the application with a user/password with create/truncate privileges</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>
<li>an <a target="_blank" href="http://httpd.apache.org/download.cgi">apache</a> WEB server and the
php-mysql module to launch the website. </li>
</ul>
</section>
<section id="downloadl">
<div class="page-header">
<h1>Download the latest copy</h1>
<h2>Download the latest copy</h2>
</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>
<p>The latest version can be downloaded from the <a href="https://mulcyber.toulouse.inra.fr/frs/?group_id=102" target="_blank">download page</a>.</p>
</section>
<section id="extract">
<div class="page-header">
<h1>Extract the archive</h1>
<h2>Extract the archive</h2>
</div>
<pre class="prettyprint linenums">
[user@hostname:~] tar xzvf jflow_v1.0.tar.gz
[user@hostname:~] cd jflow_v1.0</pre>
[user@hostname:~] tar xzvf nG6-X.X.tar.gz
[user@hostname:~] cd nG6-X.X</pre>
</section>
<section id="configure">
<div class="page-header">
<h1>Configure the application</h1>
<h2>Configure the application</h2>
</div>
<pre class="prettyprint linenums">
<ul>
<li>First you have to edit the application.properties file :
<pre class="prettyprint linenums">
[global]
# uncomment and set if not in the PATH
#makeflow = /usr/bin/makeflow
......@@ -100,39 +114,78 @@ server_socket_host = 127.0.0.1
# on which socket port should run the web server
server_socket_port = 8080
[database]
host = localhost
user = typo3
passwd = typo3
dbname = typo3
[storage]
# where should be written the log file
log_file = /path/to/jflow.log
log_file = &lt;path&gt;/ng6.log
# Where should ngspipelines data be stored
save_directory = &lt;path&gt;/ng6
# Where should the pipelines write results, should be accessible
# by all cluster nodes
work_directory = /path/to/work
work_directory = &lt;path&gt;/work
# Where should the pipelines write temporary files, should be
# accessible by all cluster nodes
tmp_directory = /path/to/tmp
tmp_directory = &lt;path&gt;/tmp
# where could be find binaries
[softwares]
# uncomment and set if not in the PATH
#
# Global softwares
#
#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>
#blastn = /usr/bin/blastn
...
</pre>
</li>
<li>Once settled, run the following command :
<pre class="prettyprint linenums">
[user@hostname:~] python bin/ng6_install.py --web-path /var/www/html/ng6 --email admin@domain</pre>
</li>
<li>To finalize the installation, go to <a href="http://127.0.0.1/ng6/index.php?id=3">http://127.0.0.1/ng6/index.php?id=3</a>, where you will have to fill the following form:
<div class="bs-docs-example" style="text-align: center;">
<img width="80%" src="img/ng6_install.png" class="img-rounded">
</div>
</li>
<li>Once filled, click on the Install NG6 button what should redirect you on the projects page. A <em>Demo project</em> should already be accessible. This project has no run for now,
those will be added during the test
<div class="bs-docs-example" style="text-align: center;">
<img width="80%" src="img/ng6_first_screen.png" class="img-rounded">
</div>
</li>
<li>From here you have a working ng6 interface. If you want to have access to your workflows from the web interface, you have to start the jflow WEB server.
<pre class="prettyprint linenums">
[user@hostname:~] python bin/jflow_server.py --daemon</pre>
This is not required since you can run your workflows from the command line.
</li>
</ul>
</section>
<section id="test">
<div class="page-header">
<h1>Test your installation</h1>
<h2>Test your installation</h2>
</div>
<p>The application embed 2 WEB site examples, enter the following command lines to run the WEB server:</p>
<p>To test your installation, the application provides embedded test files. Here are some examples of test commands :</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>
[user@hostname:~] python bin/ng6_cli.py r454_qc @workflows/r454_qc/data/r454_qc.conf --admin-login &lt;LOGIN&gt;
[user@hostname:~] python bin/ng6_cli.py illumina_rnaseq @workflows/illumina_rnaseq/data/illumina_rnaseq.conf --admin-login &lt;LOGIN&gt; </pre>
<p>All pipelines can be executed from the web interface (If the jflow server has been started). Be aware that some of the workflows
have internal prerequisits that you must configure in the application.properties file </p>
</section>
</div>
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