Adding new web service, getting rid of virtual box in docs

[jabaws.git] / website / man_serverwar.html

diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index 61801cf..0dc1ce3 100644 (file)
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -57,8 +57,7 @@
     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="#obtainexec">Obtaining alignment\r
-    programs for your operating 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="#nocluster">JABAWS on a single server</a></li>\r
@@ -185,8 +184,7 @@ Then the default configuration will work for you. More information
 about <span class="hightlight">the\r
 Executable.properties</span> file is given in the <a href="man_configuration.html#exec">JABAWS Configuration chapter.</a></p>\r
 \r
-<h3><a name="obtainexec" id="obtainexec">Obtaining alignment\r
-programs for your operating system</a></h3>\r
+<h3><a name="obtainexec" id="obtainexec">Obtaining command line binaries for your operating system</a></h3>\r
 \r
 <p>You could search for pre-packaged compiled executable in your\r
 system package repository or alternately, download pre-compiled\r
@@ -195,11 +193,13 @@ replace the executables supplied with the downloaded ones, or
 modify the paths in <span class=\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="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>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>\r
+  <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>\r
+  <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>\r
 </ul>\r
 <h3><a name="usingWsTester" id="usingWsTester"></a>Testing JABAWS Server </h3>\r
 <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>\r
@@ -243,7 +243,7 @@ modify the paths in <span class=
 </div>\r
 \r
 <!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 1 August 2011<br />\r
  Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
 Dundee, UK</div>\r
 </div>\r