📄 meme-install.html
字号:
<!---#### $Id: meme-install.html 1339 2006-09-21 19:46:28Z tbailey $#### $Log$## Revision 1.4 2006/03/07 23:30:20 nadya## merge branches v3_5_1 and v3_5_2 back to the trunk#### Revision 1.3.4.6.2.3 2006/03/01 19:04:34 nadya## add MacOS X services startup#### Revision 1.3.4.6.2.2 2006/02/22 20:49:02 nadya## enabling styling with js and css#### Revision 1.3.4.6.2.1 2006/02/16 23:25:02 nadya## add explanation for with-url flag. Needed when submitting meme output## to a remote server#### Revision 1.3.4.6 2006/02/01 02:04:47 nadya## add info for v3.5.1#### Revision 1.3.4.5 2006/01/24 20:46:50 nadya## update copyright#### Revision 1.3.4.4 2006/01/24 04:46:19 nadya## add bug issue for mast-client#### Revision 1.3.4.3 2006/01/24 01:53:08 nadya## use table for patch list#### Revision 1.3.4.2 2006/01/22 20:46:27 nadya## calrify installation options#### Revision 1.3.4.1 2006/01/19 22:54:06 nadya## Add patching info for 3.5.0#### Revision 1.3 2005/12/22 00:20:12 nadya## color commands, swap columns and rows in the table for parallel section#### Revision 1.2 2005/12/16 06:18:17 nadya## add info on checksum and database requirements#### Revision 1.1 2005/12/15 21:13:53 nadya## initial revision.## This file should go on the web download site.####---><html><head><meta http-equiv="Content-Language" content="en-us"><title>Installing the MEME System</title><script src="template-css.js" type="text/javascript"></script></head><!--<style type="text/css">ol.withroman { list-style-type: lower-roman }ol.withnum { list-style-type: arabic-numbers }span.required { color: FF4A0F}span.head { color: 004F66; text-align: center; font-weight: bold}span.command { color: 076477; font-family: helvetica; font-size: 10pt;}h1 {color: FF4A0F}h2,h3 {color: 004F66}hr { color: 004F66}table.small {cellpadding:2px; cellspacing:0px; width:50%; background-color: EFEFFF}table.large {cellpadding:2px; cellspacing:0px; width:90%; background-color: EFEFFF}th.head { color: 004F66; text-align: center; font-weight: bold}</style>--><body><script src="template-header.js" type="text/javascript"></script><center><h1><a name="top">Installing MEME</a></h1><h1>(version 3.5.0 or later)</h1></center><h3>Table of Contents:</h3><ul><li><a href="#prerequisite">Prerequisite software</a><li><a href="#getting">Getting the source</a><li><a href="#patch">Getting and installing the patches</a><li><a href="#sysrequirements">System Requirements</a><li><a href="#installingtar">Installing from a tarball</a><li><a href="#installingsvn">Installing from an SVN repository</a><li><a href="#parallel">Parallel MEME</a><li><a href="#customconfig">Customizing configuration</a><li><a href="#installexample">Installation Examples</a><li><a href="#using">Using MEME/MAST</a><li><a href="#regresstest">Running regression tests</a><li><a href="#issues">Known issues</a><li><a href="#report">Reporting problems</a></ul><hr><h2><a name="prerequisite">Prerequisite software </a></h2><p>Most of the software mentioned here is standard on many UNIX systems.To build MEME/MAST you will need:</p><ul><li>Perl (v.5.6.1 or higher) is needed to run some scripts. See <a href="http://www.perl.org">http://www.perl.org </a> for download and installation instructions.</li><li>The GNU Autoconf (version 2.53 or later)</li><li>The GNU Automake (version 1.6 or later)</li><li>Make utility</li><li>C compiler</li><li>Gzip/gunzip utilities</li></ul><p>Optional software:</p><ul><li>The CGI.pm perl module is needed if the web site is to be installed.</li><li>A Linux cluster running <b>Rocks </b> (see <a href="http://www.rocksclusters.org">http:www.rocksclusters.org </a>) or similar cluster environment. <b>Rocks</b> provides all the required and optional software.</li><li>If you want to run parallel version of MEME you will need an MPIimplementation and a batch scheduler. For MPI, one of the following: <ul> <li>LAM from <a href="http://www.lam-mpi.org">http://www.lam-mpi.org</a> <li>MPICH from <a href="http://www-unix.mcs.anl.gov/mpi/mpich">http://www-unix.mcs.anl.gov/mpi/mpich</a> </ul> For batch scheduler, one of the following: <ul> <li>SGE from <a href="http://gridengine.sunsource.net">http://gridengine.sunsource.net</a> <li>PBS from <a href="http://www.openpbs.org">http://www.openpbs.org</a> </ul></li></ul><p>[<a href="#top"> Top </a>]</p><hr><h2><a name="getting">Getting the source</a></h2><p>The current version of MEME is 3.5.1 and is available from <ahref="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>.</p><p><strong>Note:</strong>Starting with version 3.5.0, MEME has undergone a lot of changes. It is optimized and configured for running on Linux servers. It hasn't been fully tested on other platforms, and your feedback is greatly appreciated. If you'd like to wait until all the kinks to be worked out before trying the current release, please use the previous version(use version 3.0.14) from <ahref="http://meme.nbcr.net/downloads/old_versions">http://meme.nbcr.net/downloads/old_versions</a>.Installation instructions for version 3.0.14 are different and arespecified in the README file included in the release distribution meme_3.0.14.tar.gz.</p><p>The software is distributed as a source tarball<span class="command">meme_VERSION.tar.gz</span>. For each file there is a corresponding filewith the MD5 checksum: <span class="command">meme_VERSION.md5sum</span>. When downloading thesoftware, please make sure you download the corresponding checksum file and verifythat the checksum information is correct. Depending on a platform andavailable software, the verification command can be different. Here there are 3possible ways to do verification:<ol class="withnum"><li>Using md5sum command, usually available on Linux.<br><span class="command">$ md5sum meme_VERSION.tar.gz</span></li><br><li>Using md5 command, usually available on Solaris.<br><span class="command">$ md5 meme_VERSION.tar.gz</span></li><br><li>Using openssl command, usually available on any UNIX.<br><span class="command">$ openssl dgst -md5 meme_VERSION.tar.gz</span></li></ol>The output of the command (numerical part) should be exactly the same as one provided in thechecksum file. Here is the checksum information for available MEME versions:</p><center><table class="small" border=1 cellspacing=0><tr> <th class="head">File</th> <th class="head">md5sum</th></tr><tr> <td>meme_3.5.1.tar.gz</td> <td>please see <a href="http://meme.nbcr.net/downloads/meme_3.5.1.md5sum">meme_3.5.1.md5sum</a> </td></tr><tr> <td>meme_3.5.0.tar.gz</td> <td>cb552052c82c40ce3111c95f1e9697eb</td></tr><tr> <td>meme_3.0.14.tar.gz</td> <td>f18bacdce60c11bff4cde650da296228</td></tr></table></center><p>[<a href="#top"> Top </a>]</p><hr><h2><a name="patch">Getting and installing the patches</a></h2><p>The distribution may have patches associated with it. They are available from <a href="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>.The patch file name is <span class="command">filename.VERSION.patch</span>. In addition, apatched file is distributed as well and can be used as a drop-in substitutefor the original file. The drop-in file is <span class="command">filename.VERSION</span>.It is necessary to download only one of the two files depending on the method used forpatching. All patches for a specific version should be installed. The listbelow provides instructions for installation of availble patches for specificversion.</p><center><table class="large" border=1 cellspacing=0><tr> <th width=7% class="head">Version</th> <th width=25% class="head">Patch list</th> <th class="head">Installation</th></tr><tr> <td align=center>3.5.0</td> <td align=center>mast-client.txt</td> <td> <ol> <li>If downloaded a patch file <code>mast-client.txt.3.5.0.patch</code>: <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/</span> <br><span class="command"># cd meme_3.5.0/scripts/</span> <br><span class="command"># patch -p0 < mast-client.txt.3.5.0.patch </span> <br> </li> <li>If downloaded a patched file <code>mast-client.txt.3.5.0</code>: <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt</span> </li> </ol> </td></tr></table></center><p><p>[<a href="#top"> Top </a>]</p><hr><h2><a name="sysrequirements">System Requirements</a></h2><p>MEME has been used successfully on the following platforms<ul> <li><span class="head">v 3.5.1</span> <ul> <li>SunOS 5.9</li> <li>MacOS X 10.4.4 (Tiger)</li> <li>Redhat Enterprise Linux, release 4</li> <li>Cygwin (DLL 1.5.19-4.)</li> </ul> </li> <li><span class="head">v 3.5.0</span> <ul> <li>SunOS 5.9</li> <li>Redhat Enterprise Linux, release 4</li> </ul> </li></ul></p><p>Disk and memory use: </p><ul><li>Memory 10 Mb</li><li>Disk 100 Mb</li><li>Additional sufficient (approximately 26 Gb) diskspace is needed to storesequence databases required by MAST. No need if using only MEME.</li></ul><p>[<a href="#top"> Top </a>]</p><hr><h2><a name="installingtar">Installing from a tarball</a></h2><p>It is recommended to create a <strong>meme</strong> user prior to installation.Put the tarball you obtained from the web site in a directory where youwant to build the software. If the software distribution was obtainedvia SVN access please see section <a href="#installingsvn">Installing from an SVN repository</a><p><strong>0. On UNIX systems unzip and untar the distribution:</strong><br><br><span class="command">$ gunzip -c meme_VERSION.tar.gz | tar xvf - </span><br><span class="command">$ cd meme_VERSION</span></p><P>If there are patchees associated with the VERSION please see section <a href="#patch">Getting and installing the patches</a> that explains how todownload and install the patches.<p><strong>1. Configuring</strong><br><p>Run configure with specific parameters, see section <a href="#custom">Customizing configuration</a> below.<br><span class="command">$ ./configure [parameters here]</span></p><p>The most common configure command creates only command-lineversions of MEME and MAST (no web servers or clients) and connectsthe hyperlinks on the MEME HTML output to the web server at NBCR.The parameter <span class="command">prefix</span> is required,and specifies the installation directory. <br><span class="command">$ ./configure --prefix=your-install-path --with-url=http://meme.nbcr.net/meme --disable-server --disable-client</span></p><p> Without any optional parameters, command-line versions as wellas servers and clients for MEME and MAST will be installed. <br><span class="command">$ ./configure --prefix=your-install-path</span></p><p> The other possible configurations include configurations for installing a web site in addition to the server and client, or installing server and clientseparately.</p><p>To install server, client and web site on a host with a PBS or SGEbatch scheduler:⌨️ 快捷键说明
复制代码
Ctrl + C
搜索代码
Ctrl + F
全屏模式
F11
切换主题
Ctrl + Shift + D
显示快捷键
?
增大字号
Ctrl + =
减小字号
Ctrl + -