meme-install.html

EM算法的改进

<br><span class="command">$ ./configure --enable-web
--prefix=your-install-path</span></p>

<p>To install a server, client and web site on a single processor host without 
a batch scheduler:
<br><span class="command">$ ./configure --enable-web
--prefix=your-install-path
--with-queue=shell
--with-procs=1
</span></p>

<p>To configure install only client:
<br><span class="command">$ ./configure --prefix=your-install-path
--disable-server</span></p>

<p>To install only server:
<br><span class="command">$ ./configure --prefix=your-install-path
--disable-client</span></p>

<p>
<strong>2.  Compiling and installing</strong><br>
<p>To compile simply type while at the top directory:
<br><span class="command">$ make</span>

<p>If there are no errors make a test. The test will check MEME and MAST 
output against known output
<br><span class="command">$ make test</span>

<p>If there are errors, the output files from each test will be kept in
<code>tests/results/</code> and can be compared to files in <code>tests/</code>.  
When tests pass without errors the <code>results/</code> with the output files 
is removed automatically.
</p>

<p>To install the software in the directory specified by <code>prefix</code> do:
<br><span class="command">$ make install</span></p>

<p><strong>3.  Starting servers</strong>
<p>The servers should be started as user <strong>meme</strong> (or another designated user
chosen during configure step). The startup will fail if servers started by 
the superuser.</p>
<p>To start servers, execute:
<br><span class="command">$ your-install-path/bin/memed start</span></p>
<p>To check server status, execute:
<br><span class="command">$ your-install-path/bin/memed status</span></p>
<p>To stop servers, execute:
<br><span class="command">$ your-install-path/bin/memed stop</span></p>

<p>In order to start servers automatically upon reboot, startup scripts are
created during <code>make install</code> in
<code>your-install-path/etc/startup/</code>. Currently, the following scripts are
available:</p>

<p>
<center>
<table class="small" border=1  cellspacing=0>
<tr>
  <th class="head">Platform</th>
  <th class="head">Script name</th>
</tr>
<tr>
  <td>Redhat Linux</td>
  <td>meme.linux</td>
</tr>
<tr>
  <td>Solaris</td>
  <td>meme.solaris</td>
</tr>
<tr>
  <td>MacOS X</td>
  <td>Meme
  <br>StartupParameters.plist</td>
</tr>
</table>
</center>
</p>

<p>All commands below must be executed by a superuser.
<ul>
<li>For linux:
  <ol>
  <li>Copy  meme.linux into /etc/init.d/meme
  <br><span class="command"># cp your-install-path/etc/startup/meme.linux /etc/init.d/meme</span>
  <br>
  <li>Add new services for management:
  <br><span class="command"># chkconfig --add meme</span>
  <li>To start new services without reboot:
  <br><span class="command"># /etc/init.d/meme start</span>
  </ol>
<br>
<li>For Solaris:
  <ol>
  <li>Copy  meme.solaris into /etc/init.d/meme
  <br><span class="command"># cp your-install-path/etc/startup/meme.solaris /etc/init.d/meme</span>
  <br>
  <li>Add new services for management, for example:
  <br><span class="command"># ln -s /etc/init.d/meme /etc/rc2.d/K57meme</span>
  <br><span class="command"># ln -s /etc/init.d/meme /etc/rc3.d/S99meme</span>
  <li>To start new services without reboot:
  <br><span class="command"># /etc/init.d/meme start</span>
  </ol>
<br>
<li>For MacOS X:
  <ol>
  <li>Create a new directory for startup items:
  <br><span class="command"># mkdir /Library/StartupItems/Meme</span>
  <li>Copy Meme and StartupParameters.plist:
  <br><span class="command"># cp your-install-path/etc/startup/Meme /Library/StartupItems/Meme</span>
  <br><span class="command"># cp your-install-path/etc/startup/StartupParameters.plist 
                              /Library/StartupItems/Meme</span>
  <br>
  <li>To start new services without reboot:
  <br><span class="command"># /sbin/SystemStarter start Meme</span>
  </ol>

</ul>
</p>

<p>
<strong>4. Installing mast databases</strong><br>
<ul>
<li>
<p>To download the databases go to the directory that was specified with
the <code>--with-db=DBDIR</code> argument during configure step (1). If none was
given, then the default path to the database will be <code>your-install-path/db</code>. This
directory is created during <code>make install</code> step (2). For example:
<br><span class="command">$ cd install-path/db</span>

<li><p>Set the environment to get path to newly installed meme/mast executables:

<table width="70%">
<tr>
  <td width="70%"><span class="command">&nbsp;&nbsp;&nbsp;source
  your-install-path/etc/meme.csh</span></td>
  <td># for csh, tcsh</td>
</tr>
<tr >
  <td colspan="2">or</td>
</tr>
<tr>
  <td><span class="command">&nbsp;&nbsp;&nbsp;.
  your-install-path/etc/meme.sh</span></td>
  <td># for bash, sh</td>
</tr>
</table>
</p>

<li><p>Execute command to download the databases:
<br><span class="command">$ update_mast_databases [e-mail] `pwd` &lt;
your-install-path/etc/mast_db.list</span>
</ul>

<p>The resulting files in the databases directory will be around 26Gb.
It can take time to download all the databases, and the connections to some
sites from which files are downloaded may be not always available.  The result
of the download will be emailed to the address specified by <code>
[e-mail]</code>.  If there are errors, they will be noted in the
email, and the command to install the databases will need to be repeated.</p>

<p>
<strong>5. Configuring apache web access</strong><br>
<p>
This part requires  root access to create a symbolic link from the document root
directory to the web directory in MEME installation. For example, if meme
software is installed in <code>/home/meme</code>, and the HTTP
<code>DocumentRoot</code> is <code>/var/www/html</code>, then create
a link:
<br><span class="command">$ ln -s /var/www/html/meme
<install.path.here>/web</span>
</p>
<p>The URL for web access is typically <code>http://your.host.name/meme/</code>. 
Virtual hosts may be configured accordingly.
</p>
<p>[<a href="#top"> Top </a>]</p>

<hr>
<h2><a name="installingsvn">Installing from a SVN repository</a></h2>
<p>The read-write access to the SVN is granted at this point only to the
MEME developers. We provide the tarball distribution of the latest version 
on the ftp site.</p>
<p>If you have the SVN access, you can check out the source code by:
<br><span class="command">$ svn checkout svn+ssh://[e-mail]/meme/SVNROOT/trunk </span>
</p>
<p>
To start working with the distribution one needs to create a
<code>configure</code> script:
<br><span class="command">$ cd trunk</span>
<br><span class="command">$ ./bootstrap</span>
</p>
<p>
At this point, proceed with the installation as outlined in section 
<a href="#installingtar">Installing from a tarball</a> step 1. 
</p>

<p>[<a href="#top"> Top </a>]</p>

<hr>
<h2><a name="parallel">Parallel MEME</a></h2>
<p>By default, <code>configure</code> will establish if your system has the right 
software to produce parallel version of MEME. Parallel compilation is disabled if 
mpicc is not found or if batch scheduler (program <code>qsub</code>) is not found. 
Both must be present on the system.  Please see section 
<a href="prerequisite">Prerequisite software </a> for information where to get
the software.  Currently, parallel version of MEME is known to work with:</p>

<center>
<table class="small" border=1  cellspacing=0>
<tr>
  <th class="head">MPI ditributions</th>
  <th class="head">Batch Schedulers</th>
</tr>
<tr align="center">
  <td>LAM MPI</td>
  <td>SGE</td>
</tr>
<tr align="center">
  <td>MPICH</td>
  <td>PBS</td>
</tr>

</table>
</center>

<ul>
<li>If your mpicc is installed in non-standard place, use 
<code>--with-mpidir=MPIDIR</code> option when
running 'configure' to specify the MPI installation directory.  
<li>If you have a custom version of mpicc (for example, one from 
Sun HPC ClusterTools) that provides wrappers use 
<code>--with-mpicc=MPICC</code> option to specify mpicc or its wrapper by full path. 
The configure looks by default only for names 'mpicc' and 'mpcc'.
</ul>
</p>

<p>Once <code>mpicc</code> and <code>qsub</code> are located by configure, 
the parallel version of MEME, called <code>meme_p</code> is compiled and installed 
automatically via commands <code>make</code> and <code>make install</code>. 

<p>[<a href="#top"> Top </a>]</p>

<hr>
<h2><a name="customconfig">Customizing configuration</a></h2>
<p>Customization is done via the command line arguments to configure.
To find out a list and the syntax of the configurable arguments, execute:</p>
<span class="command">$ ./configure --help</span>

<p>The general syntax for all the options is one of the following:</p>
<ul>
<li>Include a <b>feature</b>:
<br>--enable-<b>feature</b>
<br>or
<br>--enable-<b>feature</b>=yes
<li>Do not include a <b>feature</b>:
<br>--disable-<b>feature</b>
<br>or
<br>--enable-<b>feature</b>=no
<li>Set a specific <b>feature</b> to a <b>value</b>: 
<br>--with-<b>feature</b>=<b>value</b>
</ul>

<p>The following table provides a list of required an optional parameters
available for <code>configure</code>. Options <span class="required">in
color</span> 
are required, the rest are optional:</p>

<!--
<table border="1" cellpadding="2" cellspacing="0" width="90%">
-->

<center>
<table class="large" border="1"  cellspacing="0">
<tr>
  <th class="head" width="30%">Option</th>
  <th class="head" width="50%">Needed for</th>
  <th class="head" >Default value</th>
</tr>
<tr>
  <td width="30%"><span class="required">--prefix</span></td>
  <td>Provide the installation location path</td>
  <td>$HOME</td>
</tr>
<tr>
  <td>--enable-debug</td>     
  <td>Produce an executable with debugging symbols</td>
  <td>no debug</td>
</tr>
<tr>
  <td>--enable-opt</td>
  <td>Produce an executable with optimization</td>
  <td>compiler and OS dependent</td>
</tr>
<tr>
  <td>--enable-serial</td>
  <td>Produce only serial executables</td> 
  <td>parallel and serial</td>
</tr>
<tr>
  <td>--enable-server</td>
  <td>Produce server executables</td> 
  <td>enabled</td>
</tr>
<tr>
  <td>--enable-client</td>
  <td>Produce client executables</td>
  <td>enabled</td>
</tr>
<tr>
  <td>--enable-web</td>
  <td>Build web site applications</td> 
  <td>disabled</td>
</tr>

<tr>
  <td>--with-queue=QUEUE</td>
  <td>QUEUE type ("sge" or "pbs" or "shell"); "shell" runs each submitted
    MEME job as a background process and should be
    used if the MEME server is running on a host without a batch scheduler.
  </td>
  <td>determined by running qstat</td>
</tr>
<tr>
  <td>--with-mpicc=MPICC</td>