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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html> <head>
<title>Generic Genome Browser</title>
<link rel="stylesheet" href="tutorial/tutorial.css">
</head>
<body>
<h1>Generic Genome Browser, v2</h1>
<a href="http://www.gmod.org/"><img src="gmod_cog.jpeg" border="0" align="RIGHT"></a>
<p>
Welcome to the Generic Genome Browser!
<h2>Documentation</h2>
<dl>
<dt><b>Online tutorial and sample data files</b></dt>
<dd><a href="tutorial/tutorial.html">/var/www/gbrowse2/tutorial<a>.</dd>
<dt><b>Installation and configuration manual</b></dt>
<dd><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a></dd>
<dt><b>Example scripts to control GBrowse from the command line</b></dt>
<dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
</dl>
<h2>Example Databases (requires gbrowse-data package)</h2>
<p>
Example in-memory databases from yeast chromosomes 1 and 2 have been
installed for you. Try them at these URL:
<ul>
<li><a href="/cgi-bin/gbrowse/gbrowse/yeast">http://your.host/cgi-bin/gbrowse/gbrowse/yeast</a> (simple example)</li>
<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_advanced">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_advanced</a> (advanced example)</li>
<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
</ul>
<p>
The "yeast_renderfarm" example will only work if a local gbrowse_slave
render slave daemon is running. To launch the daemon, run this command
as the root user:
<pre>
% /etc/init.d/gbrowse-slave start
</pre>
<h3>Alternative URLs</h3>
If you allowed the install process to adjust your Apache
configuration, you can use the alias /gb2 as an alternative to
/cgi-bin/gb2:
<ul>
<li><a href="/gb2/gbrowse/yeast">http://your.host/gb2/gbrowse/yeast</a></li>
<li><a href="/gb2/gbrowse/yeast_advanced">http://your.host/gb2/gbrowse/yeast_advanced</a></li>
<li><a href="/gb2/gbrowse/yeast_renderfarm">http://your.host/gb2/gbrowse/yeast_renderfarm</a></li>
</ul>
<h3>Accelerated Demos</h3>
By default, FastCGI and ModPerl are not set by gbrowse installation,
However, if you have FastCGI and/or ModPerl installed, you will have access to
accelerated versions of gbrowse a these URLs:
<ul>
<li>mod_fcgid
<ul>
<li><a href="/fgb2/gbrowse/yeast">http://your.host/fgb2/gbrowse/yeast</a></li>
<li><a href="/fgb2/gbrowse/yeast_advanced">http://your.host/fgb2/gbrowse/yeast_advanced</a></li>
<li><a href="/fgb2/gbrowse/yeast_renderfarm">http://your.host/fgb2/gbrowse/yeast_renderfarm</a></li>
</ul>
</li>
<li>mod_fastcgi
<ul>
<li><a href="/fast/gbrowse/yeast">http://your.host/fast/gbrowse/yeast</a></li>
<li><a href="/fast/gbrowse/yeast_advanced">http://your.host/fast/gbrowse/yeast_advanced</a></li>
<li><a href="/fast/gbrowse/yeast_renderfarm">http://your.host/fast/gbrowse/yeast_renderfarm</a></li>
</ul>
</li>
<li>mod_perl
<ul>
<li><a href="/mgb2/gbrowse/yeast">http://your.host/mgb2/gbrowse/yeast</a></li>
<li><a href="/mgb2/gbrowse/yeast_advanced">http://your.host/mgb2/gbrowse/yeast_advanced</a></li>
<li><a href="/mgb2/gbrowse/yeast_renderfarm">http://your.host/mgb2/gbrowse/yeast_renderfarm</a></li>
</ul>
</li>
</ul>
<h2>Directory Paths</h2>
<p>
For future reference, here is where you've installed GBrowse's various
components:
<dl>
<dt>GBrowse documentation, stylesheets and in-memory databases.
<dd><b>$HTDOCS</b>
<p>
<dt>GBrowse configuration files
<dd><b>$CONF</b>
<p>
<dt>Preinstalled sample database(s)
<dd><b>$DATABASES</b>
<p>
<dt>GBrowse CGI (web) scripts
<dd><ul>
<li><b>$CGIBIN/gbrowse</b>
<li><b>$CGIBIN/gbrowse_img</b>
<li><b>$CGIBIN/gbrowse_details</b>
</ul>
<p>
<dt>Temporary directories for cached images and sessions.
<dd><b>$TMP</b>
</dl>
<p>
<h2>Learning More</h2>
<p>
To find out more about Gbrowse, try the:
<ul>
<li><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a>
<li><a href="tutorial/tutorial.html">GBrowse Tutorial</a>
<!-- <li><a href="contrib/conf_files">Sample Configuration Files</a> -->
</ul>
<hr>
<address>Lincoln D. Stein, lstein@cshl.org<br>
<a href="http://www.cshl.org/">Cold Spring Harbor Laboratory</a></address>
<!-- hhmts start -->
Last modified: Thu Mar 18 18:59:16 PDT 2010
<!-- hhmts end -->
</body> </html>
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