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<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual</title>\r
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+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
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+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
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<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<li><a href="#instwar">Installing the JABAWS WAR file</a></li>\r
<li><a href="#prepexec">Preparing executables for use with JABAWS</a></li>\r
<li><a href="#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>\r
- <li><a href="#recompbinaries">Recompiling the bundled\r
- programs for your system</a></li>\r
- <li><a href="#haveexec">Reuse the binaries that are\r
- already in your system</a></li>\r
+ <li><a href="#recompbinaries">Recompiling the bundled programs for your system</a></li>\r
+ <li><a href="#haveexec">Reuse the binaries that are already in your system</a></li>\r
<li><a href="#obtainexec">Obtaining command line binaries </a><a href="#obtainexec">for your operating system</a></li>\r
<li><a href="#usingWsTester">Testing JABAWS Server</a></li>\r
<li><a href="#diffcontexts">Running many JABAWS instances on the same server</a> </li>\r
<li><a href="#clustsubsys">JABAWS supported cluster batch management systems </a></li>\r
<li><a href="#tomstopundeploy">Manually deploying JABAWS application on Apache-Tomcat </a></li>\r
</ul>\r
+\r
<p><strong>Troubleshooting</strong></p>\r
<ul>\r
<li><a href="#tomdeploy">Apache-Tomcat fails to deploy the jabaws.war file</a></li>\r
"hightlight">executable.properties</span> as described above. Below are some suggestions on where you may be able to get the binaries for your system. </p>\r
<ul>\r
<li><a href="http://www.clustal.org/omega/#Download">Clustal Omega </a></li>\r
- <li><a href="ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/">ClustalW</a></li>\r
+ <li><a href="ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.52/">ClustalW</a></li>\r
<li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a></li>\r
<li><a href="http://www.drive5.com/muscle/download3.6.html">Muscle</a></li>\r
<li><a href="http://www.tcoffee.org/Packages/Binaries/">Tcoffee</a></li>\r
<li>Restart the Tomcat, sometimes it will not since that the new war file is added without restart</li>\r
<li>If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.</li>\r
</ul>\r
-</div>\r
-\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
+</div><!-- content end-->\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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