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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
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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
+ <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> JABAWS Virtual Appliance: <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip">download</a> (520M) </li>\r
+ <li> JABAWS Virtual Appliance: <a href="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
+\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
+<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 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
+<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
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</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
+\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>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
+"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.jar">download</a> (70 K)</li>\r
+"archive/jaba-client-src-2.0.jar">download</a> (70 K)</li>\r
</ul>\r
</li>\r
</ul>\r
-<p> Help with a command line client is available from <a href="man_client.html#usingcclient">the manual pages</a>. </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 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
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<div class="body collapsed">\r
-<h3>The Complete Source Code</h3>\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
<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
+"archive/jabaws-src-2.0.jar">download</a> (250K)</li>\r
</ul>\r
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-\r
-<div id="copyright">Last update: 7 January 2011<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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