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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
- 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
+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 \r
+<a href="http://www.turnkeylinux.org">TurnKey Linux 12.1 (Tomcat edition)</a>. 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"/>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
systems over an internet, or just 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.</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="708" height="267" style="border: solid black 1px" /></p>\r
\r
-<p><strong>JABAWS appliance configuration: </strong></p>\r
-<p><strong>VMware info</strong><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 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
- - OS : TurnKey Linux, based on Ubuntu 8.0.4 JEOS (Just-Enough-Operation-System)<br />\r
- - Installation : Oracle Java 6, Tomcat 7, JABAWS v. 2.0 <br />\r
- - Hostname : tomcat <br />\r
- - IPv4 address : dhcp<br />\r
- - IPv6 address : auto<br />\r
- - DNS name : none<br />\r
- - Name server : dhcp<br />\r
- - Route : dhcp<br />\r
- - Keyboard : US_intl</p>\r
+<p><strong>JABAWS Virtual Appliance Configuration: </strong></p>\r
+<p><strong>VMware info</strong></p>\r
+<ul>\r
+ <li>CPUs : 1</li>\r
+ <li>RAM : 512 MB</li>\r
+ <li>Networking : Host only (the VM has no access to the outside network, nothing from the outside network can access the VM)</li>\r
+ <li>Hard disk : 20 GB (expanding)</li>\r
+ <li>VMware tools : Installed</li>\r
+</ul>\r
+<p><strong>OS information</strong></p>\r
+<ul>\r
+ <li>OS : TurnKey Linux (v. 12.1, <a href="http://www.turnkeylinux.org/tomcat">Standalone Tomcat</a>) based on Debian 6.0.7 (Squeeze)</li>\r
+ <li>Installation : Oracle Java 6, Tomcat 7, JABAWS v. 2.1 </li>\r
+ <li>IPv4 address : dhcp</li>\r
+ <li>IPv6 address : auto</li>\r
+ <li>DNS name : none</li>\r
+ <li>Name server : dhcp</li>\r
+ <li>Route : dhcp</li>\r
+ <li>Keyboard : US_intl</li>\r
+</ul>\r
<p><strong>Login credentials</strong><br />\r
- - Root password: jabaws</p>\r
-<p> <strong>Services</strong></p>\r
<ul>\r
- <li>Default virtual console Alt+F7 </li>\r
- <li>Tomcat web server. <br />\r
- <em>Access:</em> http://VM_IP</li>\r
- <li><strong>JABAWS URL: http://VM_IP/jabaws</strong></li>\r
- <li>Web Shell<br />\r
- <em>Access:</em> https://VM_IP:12320/</li>\r
- <li>Webmean<br />\r
- <em>Access:</em> https://VM_IP:12321/</li>\r
- <li>SSH/SFTP<br />\r
- <em>Access:</em> root@VM_IP</li>\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. </p>\r
-<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h3>\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
+ <li>Root password: jabaws</li>\r
+ <li>Tomcat admin password: adminjabaws</li>\r
+</ul>\r
+<p> <strong>Services available at the virtial machine IP (e.g. VM_IP = 172.16.232.149)</strong></p>\r
+<ul>\r
+ <li>Tomcat Web Server: http://VM_IP (e.g. http://172.16.232.149)</li>\r
+ <li>Jabaws URL: http://VM_IP/jabaws (e.g. http://172.16.232.149/jabaws)</li>\r
+ <li>Web Shell: https://VM_IP:12320/ (e.g. https://172.16.232.149:12320)</li>\r
+ <li>Webmean: https://VM_IP:12321/ (e.g. https://172.16.232.149:12321)</li>\r
+ <li>SSH/SFTP: root@VM_IP (e.g. ssh root@172.16.232.149)</li>\r
+</ul>\r
+\r
+<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</h3>\r
+<p>\r
+After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. \r
+To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> \r
+New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview \r
+<a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.\r
+</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
-<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
-\r
-<!-- content end-->\r
-<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
-</div>\r
+<h3><a name="vmiaccess" id="vmiaccess"/>VM Network Settings </h3>\r
+<p>\r
+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, \r
+but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect \r
+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 \r
+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 \r
+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 \r
+server to do that)</p>\r
+</div><!-- content end-->\r
+<div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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