95 lines
4.0 KiB
HTML
Executable File
95 lines
4.0 KiB
HTML
Executable File
<!DOCTYPE html>
|
|
<html>
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<title>Scripting Access to MEME Web Services - MEME Suite</title>
|
|
<link rel="shortcut icon" type="image/x-icon" href="images/memesuite_icon.ico">
|
|
<link rel="icon" type="image/png" href="images/memesuite_icon.png">
|
|
<link href="css/style.css" rel="stylesheet" type="text/css">
|
|
<script src="js/menu.js"></script>
|
|
</head>
|
|
<body>
|
|
<div class="memesuitelogo">
|
|
<h1>The MEME Suite</h1>
|
|
<h2>Motif-based sequence analysis tools</h2>
|
|
</div>
|
|
|
|
<h2>Scripting Access to MEME Web Services</h2>
|
|
<p>The MEME Suite web applications are exposed as SOAP Web services
|
|
through the
|
|
<a href="http://sourceforge.net/projects/opaltoolkit/">Opal toolkit</a>.
|
|
This means that you can access the MEME suite web applications from
|
|
Perl or Python scripts without having to install the MEME Suite
|
|
locally.</p>
|
|
|
|
<p>Four sample scripts that demonstrate how to submit jobs to the MEME Web
|
|
services are provided:</p>
|
|
<ul>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/MemeClient.pl">MemeClient.pl</a>
|
|
demonstrates calling the MEME web application from a Perl script.
|
|
</li>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/FimoClient.pl">FimoClient.pl</a>
|
|
demonstrates calling the FIMO web application from a Perl script.
|
|
</li>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/MemeClient.py">MemeClient.py</a>
|
|
demonstrates calling the MEME web application from a Python script.
|
|
</li>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/FimoClient.py">FimoCient.py</a>
|
|
demonstrates calling the FIMO web application from a Python script.
|
|
</li>
|
|
</ul>
|
|
<p>The scripts expect to find two data files in the working directory:</p>
|
|
<ul>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/crp0.fasta">crp0.fasta</a>
|
|
</li>
|
|
<li>
|
|
<a href="examples/sample_opal_scripts/crp0.meme.xml">crp0.meme.xml</a>
|
|
</li>
|
|
</ul>
|
|
<p>The MEME client scripts will run MEME on
|
|
<a href="examples/sample_opal_scripts/crp0.fasta">crp0.fasta</a>
|
|
and store the output in a local directory named <code>meme_out</code>.
|
|
The FIMO client scripts will run Fimo on
|
|
<a href="examples/sample_opal_scripts/crp0.meme.xml">crp0.meme.xml</a>
|
|
and
|
|
<a href="examples/sample_opal_scripts/crp0.fasta">crp0.fasta</a>
|
|
and store the output in a local directory named <code>fimo_out</code>.</p>
|
|
|
|
<p>You don't need to have a local copy of MEME Suite installed to
|
|
access the web applications from your script, but you do need to have
|
|
the appropriate version of the
|
|
<a href="http://sourceforge.net/projects/opaltoolkit/files/">Opal client libraries</a>
|
|
installed.
|
|
To install the
|
|
<a href="http://sourceforge.net/projects/opaltoolkit/files/">Opal client libraries</a>
|
|
refer to the
|
|
<a href="http://www.nbcr.net/data/docs/opal/docs/1.9/opal-perl-index.html">installation Instructions for Perl</a>
|
|
or
|
|
<a href="http://www.nbcr.net/data/docs/opal/docs/2.X/opal-py-index.html">installation instructions for Python</a>.
|
|
</p>
|
|
|
|
<p>The Perl <a href="http://sourceforge.net/projects/opaltoolkit/files/">Opal client libraries</a>
|
|
require you to have Perl 5.0.8 or higher, and you must have installed
|
|
<code>SOAP::Lite</code> 0.69 or higher.
|
|
You may need to adjust the <code>PERL5LIB</code> environment variable to
|
|
include the directory containing the Perl Opal client.</p>
|
|
|
|
<p>The demonstration scripts use the
|
|
<a href="http://meme-suite.org">MEME Web Server</a>
|
|
but you can use a local MEME web server by changing the service URL.
|
|
This is specified in the variable <code>$location</code> in the Perl script,
|
|
and in the variable <code>serviceURL</code> in the Python script.</p>
|
|
|
|
<h3>Important Note</h3>
|
|
<p>Scripting clients can easily submit enough jobs to overwhelm a MEME server,
|
|
even one with substantial hardware resources.
|
|
If you are sending jobs to a shared server, please submit only one job at a time.</p>
|
|
</body>
|
|
</html>
|
|
|