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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"><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
+<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:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
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+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
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<div id="content">\r
-<h4><a name="minclient" id="minclient"></a>JABAWS Client</h4>\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
+ <h2 id="headtitle" style="text-align:left">JABAWS Server Virtual Appliance </h2>\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> for Windows and Linux users or <a href="http://www.vmware.com/products/fusion/overview.html">VMware Fusion</a> for Mac users. <a href="http://www.jalview.org/download.html">Jalview</a></span> can <a href="man_servervm.html#jalviewWithJaba">use your local JABAWS VA</a>. </p>\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
+ <li> JABAWS Virtual Appliance: <a href="archive/jabaws-vm.zip">download</a> (520M)</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>Please check out our <a href="man_servervm.html#whenvm">manual</a> for the detailed instructions. </p>\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
+<h2><a name="jabawswar" id="jabawswar"></a>JABAWS Server Web Application </h2>\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. You can also use this version for Mac and Linux computers if you do not want to use virtualization. Finally, you can use this version with a cluster. <br/>\r
+ 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? -->\r
+ supporting at the Java servlet specification v. 2.4 or above, i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 7.0</a>. </p>\r
<ul>\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
+<li>A JABAWS WAR for all platforms (comes with precompiled Linux x86 and Windows binaries): <a href=\r
+"archive/jaba.war">download</a>\r
+(55M)</li>\r
+<li>A JABAWS WAR for Mac (comes with precompiled Mac binaries): <a href=\r
+"archive/jabaws.war">download</a> (51M)</li>\r
</ul>\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" onclick=\r
-"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
- title="Click to open/close">Packages for experts</div>\r
-\r
-<div class="body">\r
-<h4>JABAWS server without alignment programs</h4>\r
+<p>Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VA package instead. \r
+ <!-- content end-->\r
+</p>\r
\r
-<p>If you have all the programs or wish to download them\r
-separately, then this package is for you.</p>\r
+<h2> <a name="minclient" id="minclient"></a>JABAWS Command Line Client </h2>\r
+<p>The command line client is an executable Java program for scripting against JABA web services. Its also useful as an example of how to access JABAWS services if you intend to use JABAWS in your own program, with functions demonstrating how to discover command line parameters and presets supported by a service, and how to run, monitor and retrieve the results of a job. <em>Note: The client is used in the <a href="http://www.jalview.org/source/jalview_2_6_1.tar.gz">Jalview 2.6.1 source code</a> to autogenerate a graphical user interface for JABA services.</em></p>\r
<ul>\r
- <li>Complete server without native executables: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-binaries.war">\r
-download</a> (14M)</li>\r
+ <li>Command line client\r
+ <ul>\r
+ <li>binaries: <a href=\r
+"archive/min-jaba-client-2.0.jar">download</a> (80 K)</li>\r
+ <li>source: <a href=\r
+"archive/jaba-client-src-2.0.jar">download</a> (70 K)</li>\r
+ </ul>\r
+ </li>\r
</ul>\r
+<p>The command line client will display help documentation if it is run with no arguments, the same information is also given in <a href="man_client.html#usingcclient">the command line client's manual page</a>. </p>\r
+<h2>Version </h2>\r
+<p>Current JABAWS version is 2.0 release date 15 August 2011. </p>\r
+<div class="source">\r
+<div class="header collapsed" onclick=\r
+"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
+ title="Click to open/close">The Source Code</div>\r
\r
-<h4>The complete source code</h4>\r
-\r
-<p>We offer the code under <a href=\r
+<div class="body collapsed">\r
+<h2>The Complete Source Code</h2>\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
-\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>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
-\r
-<br />\r
-<br />\r
-</div>\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/jabaws-src-2.0.jar">download</a> (250K)</li>\r
+ </ul>\r
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\r
-<!-- content end-->\r
-<div id="copyright">Last update: 17 November 2010<br />\r
+</div>\r
+<!-- wrapper end-->\r
+<div id="copyright">Last update: 16 September 2011<br />\r
Peter Troshin and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
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