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<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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-<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
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<li><a href="#vboxinvalidstate">VirtualBox 4.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception </a></li>\r
<li><a href="#ovfOnVmware">VMWare Player fails to open the VM with "Fail to query source for information" exception</a></li>\r
</ul>\r
-<h3><a name="whatisvm" id="whatisvm"></a>What is JABAWS Server Virtual Appliance?</h3>\r
-<p>The JABAWS Server Virtual Appliance is an installation of JABAWS Web Application Archive (WAR) with all dependencies on TurnKey Linux within a Virtual Machine. The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">virtual appliance</a> is a way to run JABAWS server locally without the need to connect to the internet or configure JABAWS.\r
- \r
- \r
- All JABAWS clients, such as Jalview can be easily configured to use the appliance. \r
- 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> which you must install first. We have tested JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">VirtualBox v 3.2.12</a> on Windows, Linux and Mac. \r
- However, you are not limited to these virtualization systems and can use JABAWS appliance with any commercial alternative. </p>\r
-<h3><a name="whenvm" id="whenvm"/></a>When to use the virtual appliance </h3>\r
-<p>The appliance best suits users who would like to use the JABA web services locally, without an Internet connection, want to keep their data private \r
-or uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users too. However, they can always deploy a <a href="man_serverwar.html#instwar">JABAWS Server WAR distribution</a> instead. <br />\r
-The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. If you thinking of running the JABAWS server for many users and want JABAWS to use a cluster for calculations you need a WAR version of JABAWS server instead. Virtual Appliance would not be the best option for that. </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 programs such as <a href="http://www.vmware.com/products/player">VMWare Player</a> or \r
+<a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">Oracle VirtualBox 3.2.x</a>, but you will need to install them first. We have tested the JABAWS appliance \r
+with VMware Player v 3.1.2 on Windows and Linux, and <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">VirtualBox </a> v. 3.2.12 on Windows, Linux and Mac. \r
+ However, you are not limited to these virtualization systems and can use the JABAWS appliance with any commercial alternative. </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 want to access \r
+systems over an internet or local intranet connection, or alternately, want to keep their data private. It is also \r
+the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run. \r
+<br/>Since the appliance is a self contained unit of software, it is also an attractive option for Linux, UNIX or Mac users wishing to set up JABAWS services quickly.</p>\r
+<h3><a name="whennotvm" id="whennotvm"/>When <em>not</em> to use the JABAWS Virtual Appliance</h3><p>\r
+For servers that will be used heavily, we recommend that a <a href="man_serverwar.html#instwar">JABAWS Server WAR distribution</a> is deployed, rather than the Virtual Appliance version of JABAWS. \r
+This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory \r
+(where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to be sufficient for heavy computation. \r
+It is possible to reconfigure the virtual appliance so it uses more computation resources, \r
+but for most production environments, the JABAWS WAR distribution will be more easy to deploy and tune to take advantage of the resources available.</p>\r
\r
<h3><a name="howtoinstallvm" id="howtoinstallvm"></a>How to install VMWare Player or VirtualBox</h3>\r
<p>Please see the <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> \r
-and <a href="http://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox</a> web sites for up to date instructions and downloads.</p>\r
+and <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">Oracle VirtualBox</a> web sites for up to date instructions and downloads.</p>\r
\r
<h3><a name="vmplayer" id="vmplayer"/>VMware Player appliance configuration </h3>\r
<p>The free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> can be used to run the JABAWS services from the Windows and Linux host operating systems, there is no support for Mac at the time of writing (December 2010). \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)</p>\r
<h3><a name="vmbexc" id="vmbexc"/></a>VirtualBox fails to open the VM due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception</h3>\r
<p>VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such a problem, please make sure you have configured the JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all. </p>\r
-<h3><a name="vboxinvalidstate" id="vboxinvalidstate"></a>VirtualBox 4.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception </h3>\r
-<p>There were reports that VirtualBox version 4.0 suffers from this problem at least on Windows XP. The fix is to use the previous version of <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">VirtualBox 3.2.12</a></p>\r
+<h3><a name="vboxinvalidstate" id="vboxinvalidstate"></a>VirtualBox 4.0.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception </h3>\r
+<p>VirtualBox version 4.x.x is not compatible with JABAWS virtual appliance. Please download the previous version of <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">VirtualBox</a> 3.2.12 to use with JABAWS VA.</p>\r
<h3><a name="ovfOnVmware" id="ovfOnVmware"/></a>VMWare Player fails to open the VM with "Fail to query source for information" exception</h3>\r
<p>At the time of writing, the latest version of VMware Player 3.1.2 supported only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products. </p>\r
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-<div id="copyright">Last update: 7 January 2011<br />\r
+<div id="copyright">Last update: 1 April 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
git://source.jalview.org / jabaws.git / blobdiff