\r
<!-- panel end-->\r
<div id="content">\r
-<h2 align="center">JABAWS Manual</h2>\r
+<h2 id="headtitle">JABAWS Manual</h2>\r
\r
<h3>Table of content</h3>\r
<h4>JABAWS Virtual Appliance \r
</h4>\r
<ul>\r
<li><a href="#whenvm">When to use virtual appliance</a> </li>\r
+ <li><a href="#howtoinstallvm">How to install VMWare Player or VirtualBox</a> </li>\r
<li><a href="#virtualbox">VirtualBox appliance configuration</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="#warfile">JABAWS War File Content</a></li>\r
</ul>\r
<h3>JABAWS Virtual Appliance </h3>\r
-<h4><a name="whenvm" id="whenvm"/></a>When to use virtual appliance </h4>\r
-<p>The appliance best suits for individual users who want to use JABA web services locally, without Internet connection, want to keep their data private and 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 but they can always deploy a <a href="#instwar">war distribution</a> instead. <br />\r
-To run the appliance you would need to have relatively powerful computer. The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. </p>\r
+<h4><a name="whenvm" id="whenvm"/></a>When to use the virtual appliance </h4>\r
+<p>The appliance best suits users who would like to use the JABA web services locally, without an Internet connection, or want to keep their data private \r
+and 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 but they can always deploy a <a href="#instwar">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. </p>\r
+\r
+<h4><a name="howtoinstallvm" id="howtoinstallvm"></a>How to install VMWare Player or VirtualBox</h4>\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> websites for up to date instructions and downloads.</p>\r
+\r
<h4><a name="virtualbox" id="virtualbox"/>VirtualBox appliance configuration</h4>\r
-<p>VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operation systems. Use VitualBox "Import Appliance" option to import JABAWS. Please bear in mind that to benefit from multiple CPU support under VirtualBox software you need to enable<a href="http://en.wikipedia.org/wiki/X86_virtualization"> hardware virtualization extensions</a>, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine. </p>\r
-<p>We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the <a href="howto.html#vmbexc"></a><a href="howto.html#vmbexc">VERR_VMX_MSR_LOCKED_OR_DISABLED</a> exception if you computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem. </p>\r
+<p>VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operating systems. Use the VitualBox "Import Appliance" option to import the JABAWS. Please bear in mind that to benefit from multiple CPU support under the VirtualBox software you need to enable<a href="http://en.wikipedia.org/wiki/X86_virtualization"> hardware virtualization extensions</a>, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine. </p>\r
+<p>We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the <a href="howto.html#vmbexc"></a><a href="howto.html#vmbexc">VERR_VMX_MSR_LOCKED_OR_DISABLED</a> exception if your computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem. </p>\r
<p>VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.</p>\r
<p><img src="images/vmb_virtual.png" alt="VT-x extension on VirtualBox" width="669" height="535" /></p>\r
+\r
<h4><a name="vmplayer" id="vmplayer"/>VMware Player appliance configuration </h4>\r
-<p>Free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> can be used to run JABAWS services from Windows and Linux host operation system, there is no support for Mac in time of writing. However, <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial VMware product, offer virtual machine support for Mac computers too. </p>\r
-<p>To run JABAWS server on VMware player, unpack JABAWS VM into one of the folders on your local hard drive. Open VMware Player, and click "Open Virtual Machine" and point the Player to the location of the JABAWS, choose JABAWS.vmx file to open an appliance. </p>\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
+However, <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial VMware product, offers virtual machine support for Mac computers too. </p>\r
+<p>To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the JABAWS.vmx file to open an appliance. </p>\r
<p>When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all. </p>\r
+\r
<h4><a name="jabawsAppliance" id="jabawsAppliance"/>JABAWS Appliance details</h4>\r
-<p>By default, JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory let your VM deal with larger tasks, e.g. work with large alignments.</p>\r
+<p>By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.</p>\r
<p>The VMware Player screen shot below displays JABAWS VM CPU settings. </p>\r
<p><img src="images/VMware_cpu.png" alt="vmware cpu settings" width="852" height="267" border="1" /></p>\r
+\r
<p><strong>JABAWS appliance configuration: </strong></p>\r
<p><strong>VMware info</strong><br />\r
- Date of creation: 8 October 2010<br />\r
- CPUs : 1<br />\r
- RAM : 512 MB<br />\r
- - Networking : Host only (the VM has no access to the outside network, nothing from outside network can access the VM)<br />\r
+ - Networking : Host only (the VM has no access to the outside network, nothing from the outside network can access the VM)<br />\r
- Hard disk : 20 GB (expanding)<br />\r
- VMware tools : Installed</p>\r
<p><strong>OS info</strong><br />\r
</ul>\r
<p>Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. Under VirtualBox host only networking, first VM may have 192.168.56.101 IP address.</p>\r
<h4><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h4>\r
-<p>After you booted JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
+<p>After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>\r
<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>\r
<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>\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
+\r
+\r
<h3>JABAWS Installation</h3>\r
<h4><a name="sysreq" id="sysreq"></a>System Requirements</h4>\r
\r
git://source.jalview.org / jabaws.git / blobdiff