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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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-<h4><a name="minclient" id="minclient"></a>JABAWS Client</h4>\r
-\r
-<p>The client is an executable java archive which provides a\r
-command line client, and can be used by anyone who would like to\r
-program against the JABA Web Services in Java.</p>\r
-\r
-<ul>\r
-<li>JABAWS java client: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">download</a>\r
-(64k)</li>\r
-</ul>\r
+ <h2 id="headtitle" style="text-align:left">JABAWS Server Virtual Machine</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. There is also an <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">Oracle VirtualBox</a> (version 3.2.12) for Mac users. Both are free and installation is simple. <a href="http://www.jalview.org/download.html">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
\r
-<h4>JABAWS Server</h4>\r
\r
-<p>The server is provided as a self-contained web application\r
-archive containing all necessary binaries, ready to install in any\r
-'modern' Java based web application server\r
-<!-- Note - mention servlet 2.4 compliance here? -->. Download this\r
-if you intend to run JABAWS services locally.</p>\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. 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 at least version 2.4 of the Java servlet specification, i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 7.0</a>. </p>\r
\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
+(51M)</li>\r
</ul>\r
\r
\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, only the Muscle and Clustal web services will work! If you want to run the other web services on Windows, then use the JABAWS Server VM 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></ul>\r
-\r
-<h4>JABAWS server without JAX-WS</h4>\r
-\r
-<p>Download this if you intend to run JABAWS for your lab/institute\r
-locally, and have a java web application server which already has\r
-the JAX-WS libraries installed. This package does not contain <a\r
-href="https://jax-ws.dev.java.net/">JAX-WS</a> libraries, so its\r
-installation will not cause any version conflicts.<br />\r
-<em>Note: If you find the server does not work, then we suggest you\r
-try installing the full JABAWS server package.</em></p>\r
-\r
-<ul>\r
-<li>Server (without JAX-WS) for all platforms: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws.war">download</a>\r
-(31M)</li>\r
-\r
-<li>Server (without JAX-WS) for windows: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws-windows.war">\r
-download</a> (2M)</li>\r
-\r
-<li>Server (without JAX-WS) without binaries: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-no-jaxws-no-binaries.war">\r
-download</a> (<1M)</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-2.0.jar">download</a> (80 K)</li>\r
+ <li>source: <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">download</a> (70 K)</li>\r
+ </ul>\r
+ </li>\r
</ul>\r
-\r
-<h4>JABAWS execution framework</h4>\r
-\r
-<p>This package is for developers who would like to use JABAWS's\r
-execution system in their own Java programs to control native\r
-executables in local or cluster environments. It is the JABAWS code\r
-without the server components.</p>\r
-\r
-<ul>\r
-<li>The framework package: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/full-jaba-client-pack.zip">\r
-download</a>(31M)</li>\r
-</ul> \r
-\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 version 2\r
-licence</a> please feel free to download and use our product as\r
-well as the source code. The code comes in the form of an <a href=\r
-"http://www.eclipse.org">Eclipse</a> project, but Eclipse is not\r
-necessary to run it. Please examine the Ant build file (build.xml)\r
-to find out how to build JABAWS from source, and execute a variety\r
-of useful tasks, including a task for runing the JABAWS test\r
-cases.</p>\r
-\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 1.1 release date 7 April 2011. Please consult the <a href="change.log">change log</a> file for the breakdown of the changes. </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
+<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
<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>Source only package: <a href=\r
-"archive/jaba-source.jar">download</a> (25K)</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: 19 August 2010<br />\r
+</div>\r
+<!-- wrapper end-->\r
+<div id="copyright">Last update: 7 April 2011<br />\r
Peter Troshin and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
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