meme-install.html

EM算法的改进

  <td>Set MPICC to use</td>
  <td>found mpicc</td>
</tr>
<tr>
  <td>--with-mpidir=MPIDIR</td>
  <td>Set MPI installation path</td>
  <td>path of found mpicc</td>
</tr>
<tr>
  <td>--with-url=URL</td>
  <td>Set url for the web site</td>
  <td>http://<b>fqdn</b>/meme</td>
</tr>
<tr>
  <td>--with-user=USER</td>
  <td>Set user for starting the servers</td>
  <td><b>uid</b></td>
</tr>
<tr>
  <td>--with-contact=EMAIL</td>
  <td>Set email of web site administrator</td>
  <td><b>uid@fqdn</b></td>
</tr>
<tr>
  <td>--with-webdir=DIR</td>
  <td>Set path to web site part</td>
  <td>install-path/web/</td>
</tr>
<tr>
  <td>--with-db=DBDIR</td>
  <td>Set path to databases</td>
  <td>install-path/db/</td>
</tr>
<tr>
  <td>--with-logs=LOGDIR</td>
  <td>Set path to logs</td>
  <td>install-path/LOGS/</td>
</tr>
<tr>
  <td>--with-meme-port=PORT</td>
  <td>Set port to use for MEME web server</td>
  <td>3012</td>
</tr>
<tr>
  <td>--with-mast-port=PORT</td>
  <td>Set port to use for MAST web server</td>
  <td>3013</td>
</tr>
<tr>
  <td>--with-procs=PROCS</td>
  <td>Set number of processes that each MEME job started by the web server will use;
  does not affect jobs started from the command line.  Use "1" if
  the MEME server is running on a host without a batch scheduler.</td>
  <td>2</td>
</tr>
<tr>
  <td>--with-maxtime=TIME</td>
  <td>Set wall time limit (sec) a job started by the web server may use</td>
  <td>7200</td>
</tr>
<tr>
  <td>--with-qname=NAME</td>
  <td>Set queue name (needed only for PBS scheduler) web server jobs will use</td>
  <td>none</td>
</tr>
</table>
</center>

<p><b>Note 1</b>: see <a href="#parallel"> Parallel MEME</a> section for details.</p>
<p><b>Note 2</b>: in the table above <b>uid</b> refers to the UID of the user
doing installation.</p>
<p><b>Note 3</b>: in the table above <b>fqdn</b> refers to the fully qualified
hostname.</p>

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

<hr>
<h2><a name="installexample">Installation Examples</a></h2>
<ol>
<li><b>Example 1</b>: installing MEME servers and clients, including the web services in
/home/meme.
<span class="command">
<br>$ gunzip -c meme_3.5.1.tar.gz | tar xvf -
<br>$ cd meme_3.5.1
<br>$ ./configure --prefix=/home/meme --enable-web
<br>$ make
<br>$ make test
<br>$ make install
</span>

<p>After execution of these commands, provided none resulted in error,
the following directory structure will be created in /home/meme:</p>
<pre>
    bin/    db/    etc/    lib/    LOGS/    tests/    web/
</pre>
</li>

<li><b>Example 2</b>: installing MEME servers and clients without the web services in
/opt/meme.
<span class="command">
<br>$ gunzip -c meme_3.5.1.tar.gz | tar xvf -
<br>$ cd meme_3.5.1
<br>$ ./configure --prefix=/opt/meme
<br>$ make
<br>$ make check
<br>$ make install
</span>

<p>After execution of these commands, provided none resulted in error,
the following structure will be created in /opt/meme:</p>
<pre>
    bin/    db/    etc/    lib/    LOGS/    tests/
</pre>

<li><b>Example 3</b>: When installing MEME servers and clients without the web services
it is still possible to use web access to a remote server in order to submit meme output. 
In this case the users do not install the web services on a local machine.
Instead, they can specify a remote known server which will be used in MEME 
output form.  Using a remote known server will allow users to use buttons on a
MEME output form (once this output is loaded in the web browser) and submit 
the MEME results for additional processing if desired. We specifiy a 
remote server during configuration step, and
the rest of the installation is as in <b>Example 2</b> above.
<span class="command">
<br>$ ./configure --prefix=/opt/meme --with-url=http://meme.nbcr.net/meme
</span>

</ol>
</p>

<p>Directories contents:</p>
<dt><b>bin/</b></dt>  
<dd>MEME and MAST executables and scripts</dd>

<dt><b>db/</b></dt>
<dd>this directory or DIR specified by --with-db=DIR option is created.
    Initially, the database directory is empty, and is filled with the
    databases after running update_mast_databases command.</dd>

<dt><b>etc/</b></dt>
<dd>contains the following files
    <ul>
    <li>mast_db.list - databases list, for running update_mast_databases command
    <li>mast.doc, meme.doc - text files used by a few commands to provide
        usage info
    <li>meme_config - localization file, holds the variables needed for
        running scripts
    <li>prior1.plib, prior30.plib - these files are used by MEME
    <li>meme.csh - for setting user environment for tcsh or csh
    <li>meme.sh - for setting user environment for sh or bash
    </ul></dd>

<dt><b>lib/</b></dt>
<dd>contains common Perl modules</dd>

<dt><b>LOGS/</b></dt>
<dd>directory for temporary files created by mast or MEME when jobs are
    submitted via web</dd>

<dt><b>tests/</b></dt>
<dd>known correct output of MEME and MAST for specific sequences and
    databases.  These files are used when running <code>make test</code> during 
    installation or <code>bin/runtests</code></dd>

<dt><b>web/</b></dt>
<dd>contains files necessary to setup up a web-based access to MEME/MAST servers.</dd>


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

<hr>
<h2><a name="using">Using MEME/MAST</a></h2>
<p>Before using MEME and MAST, users must add a few environment variables.
All needed variables are defined in <code>meme.csh</code> and
<code>meme.sh</code> files.</p>


<ol class="withnum">
<li>If using <b>csh</b> or <b>tcsh</b>, execute the following command:
<br><span class="command">$ source install-path/etc/meme.csh   </span>

<p>To make the addition of these variables automatic upon login, add a line to your 
<code>.cshrc</code> or <code>.tcshrc</code> file:
<br><span class="command">$ source install-path/etc/meme.csh</span>   
</p>

<li>If using <b>sh</b> or <b>bash</b>, execute the following command:
<br><span class="command">$ . install-path/etc/meme.sh</span>

<p>To make the addition of these variables automatic add a line to your .profile 
or .bash_profile file:
<br><span class="command">$ . install-path/etc/meme.sh</span>
</ol>

<p>The <code>install-path</code> should be a full path to the installation directory.
To find out how to use MEME or MAST execute respectively:
<br><span class="command">$ meme </span>
<br><span class="command">$ mast </span>
</p>

<p>Both commands print usage on stdout.</p>


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

<hr>
<h2><a name="regresstest">Running regression tests</a></h2>
<p>There is a suit of tests that can be run to test MEME and MAST output
against known output. These tests can be run at any time after the installation
of newly compiled MEME and MAST binaries (meme.bin and mast.bin). These tests
can take a long time. The output files from the tests go into the newly created
directory <code>install-path/tests/results/</code>. If the tests pass without
errors this directory with its output files will be deleted. If there are
errors the output files are kept and can be compared to files in
install-path/tests/.  To run the regression tests do:</p>
<p><span class="command">$ install-path/bin/runtests</span></p>

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

<hr>
<h2><a name="issues">Known issues</a></h2>

<p><span class="head">Version 3.5.0</span></p>
<ol>
<li>Fully tested on Rocks Linux (Redhat and Cent OS).
Some users have reported configure issues with Sun and SGI platforms.
</li>

<li><p>Some users have reported confusion over the difference between</p>
<pre>
        bin/meme          and           bin/meme.csh 
</pre>
and the difference between 
<pre>
        etc/meme.csh      and           bin/meme.csh
</pre>
<p>When refactoring was taking place, a decision has been made to keep a
distinction between binary program and the shell script. In the previous
versions  they had the same name <code>meme</code>.  In 3.5.0, the binary
is <code>meme</code>, and the shell script that parses the arguments and calls
the binary is <code>meme.csh</code>. This requires a change in the command
line execution, namely typing <code>meem.csh</code> in place of <code>meme</code>.
This was deemed undesirable by some users, others pointed out that their
parsing scripts would have to change. In order to maintain compatibility with
the previous versions of MEME, the old behavior will be restored in the next
release.</p>
<p>The files <code>etc/meme.csh</code> and <code>etc/meme.sh</code> are newly introduced. 
They are created for setting user environment in a simple and uniform way.  
Please see section <a href="#using">Using MEME/MAST</a> for a reference.
</p>
</li>

<li>Option <code>--enable-web</code> is currently required to install perl
modules properly and to create <code>LOGS/</code> directory. 
</li>
<li>The file <code>bin/mast-client</code> contains a typo. Patch and installation 
instructions are available. See section 
<a href="#patch">Getting and installing the patches</a>
</li>
</ol>

<p>Fixes to these bugs and problems will be available in the next release, 
version 3.5.1.</p>

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

<hr>
<h2><a name="#report">Reporting problems</a></h2>
<p>Make sure first that you really have a problem:
<ul>
<li><strong>1.  Check your environment</strong><br>
Did you change it recently? Did you upgrade to a new version? 
Is your operating system supported?  Are you using latest
versions of tools required?
<li><strong>Look for the answers.</strong><br>
Check the INSTALL and README files that came with the distribution. 
Check the 
<a href="https://nbcr.net/forum/viewforum.php?f=5">MEME user
forum</a> if your problem has been reported and there was a solution.
Check the <a href="release_notes.html">release notes</a> for possible
bug fixes and other version-dependent changes.

<li><strong>Are you asking in the right place? </strong><br>
If your problems are related to the prerequisite software installation, 
your OS, or compiler, check relevant mailing lists, do Google search, talk
to your sysadmin. 

<li><strong>Verify what you did.</strong><br>
Often, the problem is a result of the wrong execution of the commands or
typos in the commands. Check if you executed the commands in the right order
and if they were typed properly. 

<li><strong>Report the problem.</strong><br>
If all fails and you still have the problem, go ahead and email to
<a href="mailto:[e-mail]">[e-mail]</a>.  
Here is a guiding list of what to put in your email:
<ul>
<li>Use meaningful and specific email headers
<li>Write clearly and be precise about your problem. Give as much information
as possible, yet avoid dumping large volumes of data. 
<li>Essential information to include: your OS version, the software version you are
trying to install, your compiler version,  autoconf version ...
<li>Describe the exact problem symptoms, and whether they are reproducible. 
Provide the relevant output from running <code>configure</code> or
<code>make</code> that indicates what the error was. 
</ul>
</ul>

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

<hr>
<p align="center"><b>Copyright &copy; 1994-2006 The Regents of the University of
California. All rights Reserved.</b></p>
<br><br><br>

</table>
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