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-<meta name="Last-modified" content="Mon, 11 Dec 2010 01:03:33 GMT"/>\r
+<meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual</title>\r
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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><h1><span class="headeru">JA</span>va <span class=\r
-"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
-class="headeru">S</span>ervices</h1></td>\r
+<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>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0" title="Java Bioinformatics Analysis Web Services version 2.0"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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- <a href="manual.html">Quick Start Guide</a>\r
<a href="man_about.html">About</a>\r
<a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
<a class="selected" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
<a href="man_configuration.html" >Server<br/>\r
Configuration</a>\r
<a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
<a href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>\r
JABAWS</a> \r
+ <a href="man_server_dev.html" >JABAWS Development</a>\r
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+<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
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<div id="content">\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="#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
version 2.4 of the Java Servlet specification, and a Java 6 runtime\r
environment. We recommend using an official Oracle Java 6 runtime\r
environment, and <a\r
-href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> web application server version 6, but other versions may work as well. </p>\r
+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/>\r
+<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>\r
\r
-<p>JABAWS Web Application aRchive can run on any host operating system that supports Java. However JABAWS depends on the third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform.\r
+<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.\r
<!-- todo: link to help about obtaining and installing tomcat -->\r
</p>\r
-<p>JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries and contains all the binaries sources.</p>\r
+<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>\r
<p>To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes. </p>\r
<h3><a name="instwar" id="instwar"></a>Installing the JABAWS WAR file</h3>\r
<p>JABAWS is distributed as a web application archive (WAR). To\r
deploy JABAWS in Apache-Tomcat - simply drop the war file into the\r
<span class="highlight">webapps</span> directory of a running\r
-Tomcat, and it will do the rest. If you used this deployment procedure, <span class="attention">do not remove</span> jabaws war file, otherwise Tomcat will undeploy your application! </p>\r
+Tomcat, and it will do the rest. If you used this deployment procedure, <span class="attention">do not remove</span> the jabaws WAR file, otherwise Tomcat will undeploy your application! The context path for your deployed application will be the same as the name of the war file. For example, assuming the Tomcat server is running on the <span class="hightlight">localhost:8080</span> and <strong>jaba.war</strong> file is put into the <span class="hightlight"><tomcat server root>/webapps</span> directory, the deployed application from the jaba.war file then can be accessed by this URL http://localhost:8080/<strong>jaba</strong>. </p>\r
<p>For any other web application\r
server, please follow your server's specific deployment procedure\r
for 'WAR' files. If you install JABAWS on a MS Windows machine, then\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>. with</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
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
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/linuxI386/probcons/">I386</a> | <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/binaries/linuxAMD64/probcons/">AMD64</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 <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 class="code"><?xml version="1.0" encoding="UTF-8"?><br />\r
<Context antiResourceLocking="false" privileged="true" /></p>\r
<p>This should be sufficient to prevent Tomcat from removing your JABAWS from WEBAPPS. For more information about the Tomcat deployer <a href="http://tomcat.apache.org/tomcat-6.0-doc/deployer-howto.html">read this documentation on the Apache-Tomcat web site</a>.</p>\r
-<h3><a name="tomdeploy" id="tomdeploy"></a>Apache-Tomcat fails to deploy jaba.war file </h3>\r
+<h3><a name="tomdeploy" id="tomdeploy"></a>Apache-Tomcat fails to deploy jabaws.war file </h3>\r
<ul>\r
<li>Make sure Tomcat have sufficient access rights to read your war file. </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). <a href="manual.html#setexecflag"> </a> Restart the Tomcat.</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: 7 January 2011<br />\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
git://source.jalview.org / jabaws.git / blobdiff