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-<h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices<h2>\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
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- <a class="selected" href="download.html">Download</a>\r
- <a href="http://www.jalview.org">Jalview</a>\r
+<div id="panel"><a href="index.html">Home</a> <a href=\r
+"manual.html">Manual</a> \r
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+ <h2 id="headtitle" style="text-align:left">For Users </h2>\r
+ <h3 style="margin:0;">JABAWS Server Virtual Machine </h3>\r
+ <p><span style="text-align:left">JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend <a href="http://www.vmware.com/products/player">VMWare Player</a> v 3.1 for Windows and Linux users. There is also an <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">Oracle VirtualBox</a> v. 3.2 for Mac users. Both are free and installation is simple. <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a></span> can <a href="man_servervm.html#jalviewWithJaba">use your local JABAWS VM</a>. </p>\r
+ <ul>\r
+ <li> JABAWS Virtual Appliance: <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip">download</a> (520M) </li>\r
+ </ul>\r
+ <p>Please check out our <a href="man_servervm.html#whenvm">manual</a> for the detailed instructions. </p>\r
+ <h2>For System Administrators </h2>\r
+ <h3 style="margin:0;"><a name="jabawswar" id="jabawswar"></a>JABAWS Server Web Application </h3>\r
+<p> The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. Typically, you will have a cluster or at least a powerful server machine which all users are willing to use. If you only have a single server then, you may use JABAWS Server Virtual Appliance instead. The server is provided as a self-contained <a href="http://en.wikipedia.org/wiki/WAR_(Sun_file_format)">Web Application\r
+aRchive (WAR) </a> containing all necessary binaries. WAR file can be deployed on any\r
+ web application server\r
+<!-- Note - mention servlet 2.4 compliance here? -->supporting Servlet 2.4 specification i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 6.0</a>. </p>\r
\r
-<h4><a name="minclient" id="minclient"></a>JABAWS Client</h4>\r
-<p>\r
-For anyone who would like to program against JABA Web Services or use a command line client.\r
-<a href="http://www.compbio.dundee.ac.uk/jaba/archive/min-jaba-client.jar">Download</a> (64k)</p>\r
-\r
-<h4>JABAWS Server</h4>\r
-<p>\r
-Download this if you intend to run JABAWS for your lab/university locally. \r
<ul>\r
-<li>A Complete Server for all platforms: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba.war">download</a> (45M)</li>\r
-<li>A Complete Server for windows: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-windows.war">download</a> (16M)</li>\r
+<li>A Complete Server for all platforms: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">download</a>\r
+(45M)</li>\r
</ul>\r
-</p>\r
-\r
-<div class="source">\r
-<div class="header collapsed" onclick="$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');" title="Click to open/close">Packages for experts</div> <div class="body collapsed">\r
- <h4>JABAWS server without alignment programs</h4>\r
- <p>If you have all the programs or wish to download them separately this package is for you</p>\r
- <p>Complete Server without native executables: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-binaries.war">download</a> (14M) </p>\r
- <h4>JABAWS server without JAX-WS</h4>\r
- <p>\r
- Download this if you intend to run JABAWS for your lab/institute locally. \r
- This package does not contain <a href="https://jax-ws.dev.java.net/">JAX-WS</a> libraries required to run JABAWS. This package is intended for anyone who have JAX-WS libraries already installed on their web application servers. In this case JABAWS will be using the libraries supplied by your web application server. This way you can avoid any version conflicts. </p>\r
- <ul>\r
- <li>Server for all platforms: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws.war">download</a> (31M)</li>\r
- <li>Server for windows: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-windows.war">download</a> (2M)</li>\r
- <li>Server without binaries: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-no-binaries.war">download</a> (<1M) </li>\r
- </ul>\r
\r
\r
-<h4>JABAWS framework </h4>\r
-<p>\r
-This package is for developers who would like to use JABAWS code to control native executables in local or cluster environments. It is a JABA code without web services part. \r
+<p>Please bear in mind that if you deploy JABAWS WAR on Windows only Muscle and Clustal web services will work! If you want to run other web services on Windows use JABAWS Server VM package instead. \r
+ <!-- content end-->\r
+</p>\r
+<h2>For Bioinformaticians/Developers</h2>\r
+<h3 style="margin:0;"> <a name="minclient" id="minclient"></a>JABAWS Command Line Client </h3>\r
+<p>The command line client is an executable Java program for scripting against JABA web services. If you intend to use JABAWS in your own program and need a template - download a command line client source package. You can even generate a Graphical User Interface (GUI) for JABA web services for your own program! You can consult <a href="http://www.jalview.org/source/jalview_2_6_1.tar.gz">Jalview source code</a> for a help with that. </p>\r
<ul>\r
- <li>A framework package: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/full-jaba-client-pack.zip">download</a>(31M)</li>\r
+ <li>Command line client\r
+ <ul>\r
+ <li>binaries: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">download</a> (80 K)</li>\r
+ <li>source: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source.jar">download</a> (70 K)</li>\r
+ </ul>\r
+ </li>\r
</ul>\r
-</p>\r
+<p> Help with a command line client is available from <a href="man_client.html#usingcclient">the manual pages</a>. </p>\r
+\r
+<div class="source">\r
+<div class="header collapsed" onclick=\r
+"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
+ title="Click to open/close">The Source Code</div>\r
\r
-<h4>A complete source code</h4>\r
-<p>We offer the code under <a href="http://www.apache.org/licenses/LICENSE-2.0.txt">Apache version 2 licence</a> please feel free to download and use our product as well as the source code.\r
-Code comes in the form of an <a href="http://www.eclipse.org">Eclipse</a> project. However, Eclipse is not necessary to run it. Look into build.xml Ant task to find a variety of useful tasks among them are the tasks to run test cases.\r
+<div class="body collapsed">\r
+<h3>The Complete Source Code</h3>\r
+<p>If you want to add another web service or modify JABAWS in any way just download a complete JABAWS source code. We offer the code under <a href=\r
+"http://www.apache.org/licenses/LICENSE-2.0.txt">Apache licence</a>. The code archive contains the complete <a href=\r
+"http://www.eclipse.org">Eclipse</a> JABAWS project, but Eclipse is not\r
+ necessary to build it. Please examine the Ant build file (build.xml)\r
+ to build and test JABAWS from sources.</p>\r
<ul>\r
- <li>\r
-A complete eclipse project package: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-project.zip">download</a> (82M)</li>\r
- <li>Source only package: <a href="archive/jaba-source.jar">download</a> (25K) </li>\r
-</ul>\r
-</p>\r
-</div><!--body end -->\r
-</div> <!--source end -->\r
+ <li>A complete Eclipse project package: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-project.zip">download</a> (82M)</li>\r
+ <li>JABAWS source only package: <a href=\r
+"archive/jaba-source.jar">download</a> (250K</li>\r
+ </ul>\r
+\r
+<!--body end -->\r
+</div>\r
+\r
+<!--source end -->\r
</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 7 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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-</div> <!-- page end-->\r
\r
+\r
+<div id="copyright">Last update: 7 January 2011<br />\r
+ Peter Troshin and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
+</div>\r
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