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<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h2>JABAWS Server Virtual Appliance</h2>\r
<ul>\r
- <li><a href="#whatisvm">What is JABAWS Virtual Appliance?</a></li>\r
- <li><a href="#whenvm">When to use virtual appliance</a> </li>\r
- <li><a href="#howtoinstallvm">How to install VMware Player </a></li>\r
- <li><a href="#vmplayer">VMware Player appliance configuration </a></li>\r
- <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>\r
- <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>\r
- <li><a href="#vmiaccess">VM Network Settings </a></li>\r
- </ul>\r
+ <li><a href="#whatisvm">What is JABAWS Virtual Appliance?</a></li>\r
+ <li><a href="#whenvm">When to use virtual appliance</a> </li>\r
+ <li><a href="#howtoinstallvm">How to install VMware Player </a></li>\r
+ <li><a href="#vmplayer">VMware Player appliance configuration </a></li>\r
+ <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>\r
+ <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>\r
+ <li><a href="#vmiaccess">VM Network Settings </a></li>\r
+</ul>\r
\r
<p> </p>\r
<h3><a name="whatisvm" id="whatisvm"></a>What is the JABAWS Server Virtual Appliance?</h3>\r
<p>The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">Virtual Appliance</a> is a \r
way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. \r
-What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), running an installation of the JABAWS \r
-Web Application Archive (WAR) on TurnKey Linux. Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it.<br/>\r
-You can run the appliance with freely available program such as <a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it first. We have tested the JABAWS appliance \r
-with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. \r
+What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), \r
+running an installation of the JABAWS Web Application Archive (WAR) on TurnKey Linux. Once this has \r
+started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS \r
+client (such as Jalview or the JABAWS command line client) to connect to it.<br/>\r
+You can run the appliance with freely available program such as \r
+<a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it \r
+first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and \r
+VMware Fusion on Mac. \r
However, you are not limited to these virtualization systems and can use the JABAWS appliance with any other virtualization platform. You can use <a href="http://communities.vmware.com/community/vmtn/server/vsphere/automationtools/ovf">VMware OVF tool</a> to prepare JABAWS image for a different virtualization platform e.g. <a href="http://www.virtualbox.org/">VirtualBox</a>.</p>\r
<h3><a name="whenvm" id="whenvm"/></a>When to use the JABAWS Virtual Appliance</h3>\r
<p>The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access \r
<p>If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.</p>\r
<h3><a name="vmiaccess" id="vmiaccess"/></a></a>VM Network Settings </h3>\r
<p>By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)</a></p>\r
-</div>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
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