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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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+<table> \r
+<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"><h2><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</h2></td>\r
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-\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
+<p>The command line client is an executable Java program which can use JABAWS. It is good for scripting against JABA web services. If you prefer point-and-click interface - download the Graphical User Interface (GUI) client, the <a href="http://www.jalview.org">Jalview</a>. If you intend to write you own client and need a template - download a command line client source package. For a help on generating GUI's for JABA web services you can consult <a href="http://www.jalview.org/source/jalview_2_6_1.tar.gz">Jalview source code</a>. </p>\r
+\r
+<ul>\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
+<li>GUI client \r
+ (Jalview)\r
+ <ul>\r
+ <li>binaries: <a href=\r
+"http://www.jalview.org/Web_Installers/install.htm">download</a> (18 Mb)</li>\r
+ </ul>\r
+</li>\r
+</ul>\r
+\r
+<p>Please refer to <a href="http://www.jalview.org/help.html">Jalview help pages</a> for a help on connecting to JABAWS instance. Help with a command line client is available from <a href="howto.html#usingcclient">How To</a> pages. </p>\r
<h4>JABAWS Server</h4>\r
-<p>\r
-Download this if you intend to run JABAWS for your lab/university locally. \r
+\r
+<p>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>. Download this\r
+if you intend to run JABAWS services locally.</p>\r
+\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
+\r
+<li>A Complete Server for Windows: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-windows.war">download</a>\r
+(16M)</li>\r
</ul>\r
-</p>\r
\r
+\r
+<p>Please bear in mind that server for Windows supports only Muscle and Clustal web services! Please refer to the <a href="howto.html#jabaonwin">how to</a> pages to find out why. If you want to run other web services on Windows choose Virtual Appliance package below. </p>\r
+<h4>A JABAWS Server Virtual Appliance </h4>\r
+<p>JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">virtual appliance</a> is a complete installation of JABAWS software on <a href="http://www.turnkeylinux.org/">TurnKey Linux</a>. By using virtual appliance you can completely avoid JABAWS installation. The appliance comes fully configured to run JABAWS. All JABAWS clients, such as Jalview can be easily configured to use the appliance. You can run the appliance with freely available <a href="http://www.vmware.com/products/player">VMWare Player</a> or <a href="http://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox.</a> We have tested JABAWS appliance with VMWare Player on Windows and Linux, and VirtualBox on Windows, Linux and Mac. However, you are not limited to these virtualization systems and can use JABAWS appliance with any commercial alternative. </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 review the relevant <a href="manual.html#whenvm">manual</a> and <a href="howto.html#vmbexc">how to</a> sections for the configuration settings. </p>\r
+<p> </p>\r
<div class="source">\r
-<div class="header collapsed" onclick="$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');" title="Click to open/close">Packages for experts</div> <div class="body collapsed">\r
- <h4>JABAWS server without alignment programs</h4>\r
- <p>If you have all the programs or wish to download them separately this package is for you</p>\r
- <p>Complete Server without native executables: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-binaries.war">download</a> (14M) </p>\r
- <h4>JABAWS server without JAX-WS</h4>\r
- <p>\r
- Download this if you intend to run JABAWS for your lab/institute locally. \r
- This package does not contain <a href="https://jax-ws.dev.java.net/">JAX-WS</a> libraries required to run JABAWS. This package is intended for anyone who have JAX-WS libraries already installed on their web application servers. In this case JABAWS will be using the libraries supplied by your web application server. This way you can avoid any version conflicts. </p>\r
- <ul>\r
- <li>Server for all platforms: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws.war">download</a> (31M)</li>\r
- <li>Server for windows: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-windows.war">download</a> (2M)</li>\r
- <li>Server without binaries: <a href="http://www.compbio.dundee.ac.uk/jaba/archive/jaba-no-jaxws-no-binaries.war">download</a> (<1M) </li>\r
- </ul>\r
-\r
-\r
-<h4>JABAWS framework </h4>\r
-<p>\r
-This package is for developers who would like to use JABAWS code to control native executables in local or cluster environments. It is a JABA code without web services part. \r
+<div class="header" onclick=\r
+"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
+ title="Click to open/close">Packages for experts</div>\r
+\r
+<div class="body">\r
+<h4>JABAWS server without alignment programs</h4>\r
+\r
+<p>If you have all the programs or wish to download them\r
+separately, then this package is for you.</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>Complete server without native executables: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-binaries.war">\r
+download</a> (14M)</li>\r
</ul>\r
-</p>\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
+<h4>The complete source code</h4>\r
+\r
+<p>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
+\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
+<li>A complete Eclipse project package: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-project.zip">download</a>\r
+(82M)</li>\r
+\r
+<li>JABAWS source only package: <a href=\r
+"archive/jaba-source.jar">download</a> (250K)</li>\r
</ul>\r
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-<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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+\r
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+\r
+<!-- content end-->\r
+<div id="copyright">Last update: 17 November 2010<br />\r
+ Peter Troshin and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
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