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-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual</title>\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
\r
<h3><a name="useprebin" id="useprebin"></a>Using the pre-compiled i386 binaries on Linux</h3>\r
\r
-<p>Before the binaries that are bundled with JABAWS can be used,\r
-they must first be made executable using the provided <a name=\r
-"setexecflag" id="setexecflag">'setexecflag.sh'</a> script:</p>\r
-\r
-<ol>\r
-<li>cd to <span class=\r
-"hightlight"><webapplicationpath>/binaries/src</span></li>\r
-\r
-<li>run <span class="hightlight">sh setexecflag.sh</span></li>\r
-\r
-<li>Make sure binaries supplied work under your OS.<br />\r
- For this run each binary, without any command line options or\r
+<p>JABAWS comes with pre-compiled x86 Linux binaries, thus on such systems JABAWS should work straight out of the box. If you are in any doubts or experience problems you may want to make sure that the binaries supplied work under your OS. To do this just execute each binary, without any command line options or\r
input files. If you see an error message complaining about missing\r
libraries or other problems, then you probably need to <a href=\r
-"#recompbinaries">recompile the binaries</a>.</li>\r
-\r
-<li>Restart the Tomcat.</li>\r
-</ol>\r
+"#recompbinaries">recompile the binaries</a>.</p>\r
\r
-That's it! JABAWS should work at this point. Try it out using the JABAWS<a\r
-href="#usingWsTester"> test client</a>. If not,\r
-read on... or have a look at <a href="http://tomcat.apache.org/tomcat-6.0-doc/deployer-howto.html">deploying on Tomcat</a> tips.<br />\r
+You can try the JABAWS functionality with the JABAWS<a\r
+href="#usingWsTester"> test client</a> or have a look at <a href="http://tomcat.apache.org/tomcat-6.0-doc/deployer-howto.html">deploying on Tomcat</a> tips if you experience any problems.<br />\r
<em>Note: You may want to enable logging, <a href="man_configuration.html#logfiles"> as described here</a></em>.<br />\r
\r
\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>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 <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type:<span class="code"> java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path></span></p>\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></p>\r
+<p><strong>Using JABAWS service status checker</strong></p>\r
+<p>If you see it, then it is time to make sure that web services are working too. The easiest way to do so is to access Services Status page available from the main JABAWS web page menu. </p>\r
+<p>If you need to monitor web service health automatically when the best option is to use service checker that responds with the standard HTTP status code. To access this checker use the following URL: <span class="code"><jabaws_server>/HttpCodeResponseServiceStatus</span> This page returns code 200, and no page context if all services are operational, 503 if one of the services have problems. You can also check each web service individually by providing the name of the web service to check at the end of the service checker URL like this: <span class="code"><jabaws_server>/HttpCodeResponseServiceStatus/ClustalWS</span></p>\r
+<p>Upon request, the service status checker will examine the health of the ClustalWS web service only. If the service name is not valid, then the service checker will return code 400. </p>\r
+<p><strong>Using command line client</strong> </p>\r
+<p>Alternatively, you should be able to use the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type:<span class="code"> java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path></span></p>\r
<p>For example to test all JABAWS web services on host myhost.compbio.ac.uk type: </p>\r
<p class="code">java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws </p>\r
<p>You can choose a particular web server using -s option like this <span class="code">java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS </span>This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory.</p>\r
<p><span class="code">Connecting to service ProbconsWS on http://localhost:8080/ws ... OK<br />\r
Testing alignment with default parameters:FAILED<br />\r
Service ProbconsWS IS NOT FUNCTIONAL</span>If the web server did not respond the message looks like following: <span class="code">Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED</span></p>\r
-<h3><a name="diffcontexts" id="diffcontexts"/></a></a>Running many JABAWS instances on the same server</h3>\r
+<h3><a name="diffcontexts" id="diffcontexts"/>Running many JABAWS instances on the same server</h3>\r
<p> JABAWS is supplied as a Web Application aRchive which can be dealt with as any other web applications. So it is perfectly possible to run two JABAWS instances from the same server. Just make two different contexts on your application server and unpack JABAWS in both of them. For example if your server name is http://www.align.ac.uk, and the context names are public and private. Than one group of users could be given a URL http://www.align.ac.uk/public and another http://www.align.ac.uk/private. These contexts will be served by two independent JABAWS instances, and could be configured differently. If you keep local engine enabled, make sure you reduce the number of threads local engine is allowed to use to avoid overloading the server. Alternatively two completely separate web application server instances (e.g. Apache-Tomcat) could be used. This will give you a better resilience and more flexibility in memory settings. </p>\r
<h3><a name="nocluster" id="nocluster"></a>JABAWS on a single server</h3>\r
<p>You can run JABAWS on a single server. Obviously the capacity will be limited, but may be sufficient for a small lab. Installed on a single server, JABAWS executes tasks in parallel, so the more cores the server has the more requests it will be able to handle. </p>\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
+</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
+</div><!-- wrapper end-->\r
+</div><!-- page end-->\r
\r
-<!-- content end-->\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
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