X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fman_serverwar.html;h=57e54a1ab0f472075e1cd56b411c3d7cbbfa7ad1;hb=0d3b931076cf21ff2800c2de77d72f81efa5a7e5;hp=8ce8d2432ad7189b8548a78a658d3c47146b970d;hpb=93d0708fdc3ee19fcfc2e4fe7df98e861aba3501;p=jabaws.git

diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index 8ce8d24..57e54a1 100644
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -15,11 +15,12 @@
 <div id="page">
 <div id="banner">
 <table> 
-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif"  alt="University of Dundee" class="logo"  title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>
-<td class="bg"><img src="images/align.png"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif"  alt="University of Dundee" width="158" height="90" class="logo"  title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
 </tr>
-</table></div><!-- banner end-->
+</table>
+</div><!-- banner end-->
 
 <div id="wrapper">
 <div id="panel"><a href="index.html">Home</a> 
@@ -28,17 +29,20 @@
 	<div id="submenu">
 		<a href="man_about.html">About</a>
 		<a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>
+		<a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>
 		<a class="selected" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>
 		<a href="man_configuration.html" >Server<br/>
 		Configuration</a>
 		<a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>
+		<a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>
 		<a href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>
 		JABAWS</a>	
+		<a href="man_server_dev.html" >JABAWS Development</a>
 	</div>
 <a href="download.html">Download</a> 
 <a href="contacts.html">Contact Us</a>
-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> 
-</div>
+<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>
 
 <!-- panel end-->
 <div id="content">
@@ -54,8 +58,7 @@
     programs for your system</a></li>
   <li><a href="#haveexec">Reuse the binaries that are
     already in your system</a></li>
-  <li><a href="#obtainexec">Obtaining alignment
-    programs for your operating system</a></li>
+  <li><a href="#obtainexec">Obtaining command line binaries </a><a href="#obtainexec">for your operating system</a></li>
   <li><a href="#usingWsTester">Testing JABAWS Server</a></li>
   <li><a href="#diffcontexts">Running many JABAWS instances on the same server</a> </li>
   <li><a href="#nocluster">JABAWS on a single server</a></li>
@@ -71,12 +74,13 @@
 version 2.4 of the Java Servlet specification, and a Java 6 runtime
 environment. We recommend using an official Oracle Java 6 runtime
 environment, and <a
-href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> web application server version 6, but other versions may work as well.<br/><span class="attention">Please Note:</span> The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.</p>
+href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a> web application server version 7, but older Tomcat versions above 5.5 would work too.<br/>
+<span class="attention">Please Note:</span> The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.</p>
 
-<p>JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform.
+<p>JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, not all web services are currently available for MS Windows platform.
   <!-- todo: link to help about obtaining and installing tomcat -->
 </p>
-<p>JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries, as well as the source code and build scripts necessary to recompile them.</p>
+<p>JABAWS comes with pre-compiled MS Windows and Linux x86 binaries, as well as the source code and build scripts necessary to recompile them.</p>
 <p>To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes. </p>
 <h3><a name="instwar" id="instwar"></a>Installing the JABAWS WAR file</h3>
 <p>JABAWS is distributed as a web application archive (WAR). To
@@ -182,8 +186,7 @@ Then the default configuration will work for you. More information
 about <span class="hightlight">the
 Executable.properties</span> file is given in the <a href="man_configuration.html#exec">JABAWS Configuration chapter.</a></p>
 
-<h3><a name="obtainexec" id="obtainexec">Obtaining alignment
-programs for your operating system</a></h3>
+<h3><a name="obtainexec" id="obtainexec">Obtaining command line binaries for your operating system</a></h3>
 
 <p>You could search for pre-packaged compiled executable in your
 system package repository or alternately, download pre-compiled
@@ -192,11 +195,13 @@ replace the executables supplied with the downloaded ones, or
 modify the paths in <span class=
 "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>
 <ul>
+  <li><a href="http://www.clustal.org/omega/#Download">Clustal Omega </a></li>
   <li><a href="ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/">ClustalW</a></li>
   <li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a></li>
   <li><a href="http://www.drive5.com/muscle/download3.6.html">Muscle</a></li>
   <li><a href="http://www.tcoffee.org/Packages/Binaries/">Tcoffee</a></li>
-  <li>Probcons (Linux <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x86/probcons">x86</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x64/probcons">x64</a>)</li>
+  <li>Probcons (Linux <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x86/probcons">x86</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x64/probcons">x64</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/mac/probcons">Mac</a>)</li>
+  <li>IUPred (Linux <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x86/iupred">x86</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linux_x64/iupred">x64</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/mac/iupred">Mac</a>)</li>
 </ul>
 <h3><a name="usingWsTester" id="usingWsTester"></a>Testing JABAWS Server </h3>
 <p>First of all make sure that Tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your Tomcat JABAWS context path e.g. <span class="code">http://myhost.compbio.ac.uk:8080/jabaws</span>If you see it, then it is time to make sure that web services are working too. Assuming that you have unpacked/deployed JABAWS from the server war file, you should be able to navigate to the test program which can be found in &lt;webapplicationpath&gt;/WEB-INF/lib/jabaws-client.jar file. To run the tests type:<span class="code"> java -jar jabaws-client.jar -h=&lt;Your web application server host name, port and JABAWS context path&gt;</span></p>
@@ -240,7 +245,7 @@ modify the paths in <span class=
 </div>
 
 <!-- content end-->
-<div id="copyright">Last update: 1 April 2011<br />
+<div id="copyright">Last update: 1 August 2011<br />
  Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of
 Dundee, UK</div>
 </div>