website/man_servervm.jsp

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  11         <c:param name="title">Documentation</c:param>
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  13
  14 <ol class="breadcrumb">
  15         <li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
  16         <li><a href="man_docs.jsp">Documentation</a></li>
  17         <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
  18 </ol>
  19 <div class="row">
  20         <div class="col-md-12">
  21                 <div class="panel panel-default">
  22                         <div class="panel panel-heading">
  23                                 <h1 class="panel-title">Virtual Appliance</h1>
  24                         </div>
  25                         <div class="panel-body">
  26                                 <!--<h4>JABAWS Server Virtual Appliance</h4>-->
  27                                 <ul>
  28                                         <li><a href="#whatisvm">What is JABAWS Virtual Appliance?</a></li>
  29                                         <li><a href="#whenvm">When to use the Virtual Appliance</a> </li>
  30                                         <li><a href="#howtoinstallvm">How to install VMware Player </a></li>
  31                                         <li><a href="#vmplayer">VMware Player Appliance configuration </a></li>
  32                                         <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>
  33                                         <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>
  34                                         <li><a href="#vmiaccess">VM Network Settings </a></li>
  35                                 </ul>
  36                                 <!--<p class="justify">-->
  37                                 <!--</p>-->
  38                         </div>
  39                 </div>
  40         </div>
  41 </div>
  42
  43 <div class="row" id="whatisvm">
  44         <div class="col-md-12">
  45                 <div class="panel panel-default">
  46                         <div class="panel panel-heading">
  47                                 <h1 class="panel-title">What is JABAWS Virtual Appliance?</h1>
  48                         </div>
  49                         <div class="panel-body">
  50                                 <p class="justify">The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">Virtual Appliance</a> is a
  51                                         way to run a JABAWS server locally, without the need to connect to the internet or configure JABAWS.
  52                                         What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM),
  53                                         running an installation of the JABAWS Web Application Archive (WAR) on
  54                                         <a href="http://www.turnkeylinux.org">TurnKey Linux 12.1 (Tomcat edition)</a>. Once this has
  55                                         started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS
  56                                         client (such as Jalview or the JABAWS command line client) to connect to it.<br/>
  57                                         You can run the appliance with freely available program such as
  58                                         <a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it
  59                                         first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and
  60                                         VMware Fusion on Mac.
  61                                         However, you are not limited to these virtualization systems and can use the JABAWS Appliance with
  62                                         any other virtualization platform. You can use
  63                                         <a href="http://communities.vmware.com/community/vmtn/server/vsphere/automationtools/ovf">VMware
  64                                                 OVF tool</a> to prepare JABAWS image for a different virtualization platform e.g.
  65                                         <a href="http://www.virtualbox.org/">VirtualBox</a>.
  66                                 </p>
  67                                 <p class="text-right">
  68                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
  69                                 </p>
  70                         </div>
  71                 </div>
  72         </div>
  73 </div>
  74 <div class="row" id="whenvm">
  75         <div class="col-md-12">
  76                 <div class="panel panel-default">
  77                         <div class="panel panel-heading">
  78                                 <h1 class="panel-title">When to use the Virtual Appliance</h1>
  79                         </div>
  80                         <div class="panel-body">
  81                                 <p class="justify">The appliance best suits users who would like to use the JABAWS web-services locally.
  82                                         This might be because they do not want to access
  83                                         systems over an internet, or just  want to keep their data private. It is also
  84                                         the recommended option for users who want to install JABAWS on Windows, which does not support all the
  85                                         bioinformatics programs that JABAWS can run.
  86                                 </p>
  87
  88                                 <p class="justify">
  89                                         For servers that will be used heavily, we recommend that a
  90                                         <a href="man_serverwar.jsp#instwar">JABAWS Server WAR distribution</a> is deployed, rather than the
  91                                         Virtual Appliance version of JABAWS.
  92                                         This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory
  93                                         (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to
  94                                         be sufficient for heavy computation.
  95                                         It is possible to reconfigure the virtual appliance so it uses more computation resources,
  96                                         but for most production environments, the JABAWS WAR distribution will be  easier to deploy and fine
  97                                         tune to take advantage of the available resources.
  98                                 </p>
  99                                 <p class="text-right">
 100                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 101                                 </p>
 102                         </div>
 103                 </div>
 104         </div>
 105 </div>
 106 <div class="row" id="howtoinstallvm">
 107         <div class="col-md-12">
 108                 <div class="panel panel-default">
 109                         <div class="panel panel-heading">
 110                                 <h1 class="panel-title">How to install VMware Player</h1>
 111                         </div>
 112                         <div class="panel-body">
 113                                 <p class="justify">
 114                                         Please see the <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a>
 115                                         web sites for up to date instructions and downloads.
 116                                 </p>
 117                                 <p class="text-right">
 118                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 119                                 </p>
 120                         </div>
 121                 </div>
 122         </div>
 123 </div>
 124 <div class="row" id="vmplayer">
 125         <div class="col-md-12">
 126                 <div class="panel panel-default">
 127                         <div class="panel panel-heading">
 128                                 <h1 class="panel-title">VMware Player Appliance configuration</h1>
 129                         </div>
 130                         <div class="panel-body">
 131                                 <p class="justify">The free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a>
 132                                         can be used to run the JABAWS services from the Windows and Linux host operating systems.
 133                                         <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial
 134                                         VMware product, offers virtual machine support for Mac.
 135                                 </p>
 136                                 <p class="justify">To run the JABAWS server on VMware player,  unpack the JABAWS VM into one of the folders on
 137                                         your local hard drive. Open VMware Player, click &quot;Open Virtual Machine&quot; and point
 138                                         the Player to the location of the JABAWS, then choose the JABAWS.vmx file to open an appliance.
 139                                 </p>
 140                                 <p class="justify">When you play the machine for the first time the Player might ask you whether &quot;This
 141                                         virtual machine may have been moved or copied.&quot;,  say that you have copied it.
 142                                         That is all.
 143                                 </p>
 144
 145                                 <p class="text-right">
 146                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 147                                 </p>
 148                         </div>
 149                 </div>
 150         </div>
 151 </div>
 152 <div class="row" id="jabawsAppliance">
 153         <div class="col-md-12">
 154                 <div class="panel panel-default">
 155                         <div class="panel panel-heading">
 156                                 <h1 class="panel-title">JABAWS Appliance details</h1>
 157                         </div>
 158                         <div class="panel-body">
 159                                 <p class="justify">By default, the JABAWS virtual appliance is configured with 512M
 160                                         of memory and 1 CPU, but you are free to change these settings. If you have
 161                                         more than one CPU or CPU core on your computer you can make them available
 162                                         for the JABAWS virtual machine by editing virtual machine settings. Please
 163                                         bear in mind that more CPU power will not make a single calculation go faster,
 164                                         but it will enable the VM to do calculations in parallel. Similarly, you can
 165                                         add more memory to the virtual machine. More memory lets your VM deal with
 166                                         larger tasks, e.g. work with large alignments.
 167                                 </p>
 168                                 <p class="justify">
 169                                         The VMware Player screen shot below displays JABAWS VM CPU settings.
 170                                 </p>
 171                                 <p>
 172                                         <img src="static/img/VMware_cpu.png" alt="vmware cpu settings" width="708"
 173                                                  height="267" style="border: solid black 1px" />
 174                                 </p>
 175
 176                                 <p><strong>JABAWS Virtual Appliance Configuration: </strong></p>
 177                                 <p><strong>VMware info</strong></p>
 178                                 <ul>
 179                                         <li>CPUs : 1</li>
 180                                         <li>RAM : 512 MB</li>
 181                                         <li>Networking : Host only (the VM has no access to the outside network, nothing from the
 182                                                 outside network can access the VM)</li>
 183                                         <li>Hard disk : 20 GB  (expanding)</li>
 184                                         <li>VMware tools : Installed</li>
 185                                 </ul>
 186                                 <p><strong>OS information</strong></p>
 187                                 <ul>
 188                                         <li>OS : TurnKey Linux (v. 12.1, <a href="http://www.turnkeylinux.org/tomcat">Standalone
 189                                                 Tomcat</a>) based on Debian 6.0.7 (Squeeze)</li>
 190                                         <li>Installation : Oracle Java 6, Tomcat 7, JABAWS v. 2.1 </li>
 191                                         <li>IPv4 address : dhcp</li>
 192                                         <li>IPv6 address : auto</li>
 193                                         <li>DNS name : none</li>
 194                                         <li>Name server : dhcp</li>
 195                                         <li>Route : dhcp</li>
 196                                         <li>Keyboard : US_intl</li>
 197                                 </ul>
 198                                 <p><strong>Login credentials</strong><br />
 199                                 <ul>
 200                                         <li>Root password: jabaws</li>
 201                                         <li>Tomcat admin password: adminjabaws</li>
 202                                 </ul>
 203                                 <p>  <strong>Services available at the virtial machine IP (e.g. VM_IP = 172.16.232.149)</strong></p>
 204                                 <ul>
 205                                         <li>Tomcat Web Server: http://VM_IP (e.g. http://172.16.232.149)</li>
 206                                         <li>Jabaws URL: http://VM_IP/jabaws (e.g. http://172.16.232.149/jabaws)</li>
 207                                         <li>Web Shell: https://VM_IP:12320/ (e.g. https://172.16.232.149:12320)</li>
 208                                         <li>Webmean: https://VM_IP:12321/ (e.g. https://172.16.232.149:12321)</li>
 209                                         <li>SSH/SFTP: root@VM_IP (e.g. ssh root@172.16.232.149)</li>
 210                                 </ul>
 211                                 <p class="text-right">
 212                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 213                                 </p>
 214                         </div>
 215                 </div>
 216         </div>
 217 </div>
 218 <div class="row" id="jalviewWithJaba">
 219         <div class="col-md-12">
 220                 <div class="panel panel-default">
 221                         <div class="panel panel-heading">
 222                                 <h1 class="panel-title">Configuring Jalview to work with your JABAWS VM</h1>
 223                         </div>
 224                         <div class="panel-body">
 225
 226                                 <p class="justify">
 227                                         After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different.
 228                                         To enable Jalview to work with your JABAWS appliance you need to go to Jalview-&gt;Tools-&gt;Preferences-&gt;Web Services -&gt;
 229                                         New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview
 230                                         <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.
 231                                 </p>
 232                                 <p><img src="static/img/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734"
 233                                                 height="461" /></p>
 234                                 <p class="justify">If you click on Advanced Menu, you will see the configuration console,
 235                                         similar to the one below.
 236                                 </p>
 237                                 <p><img src="static/img/VMware_booted.png" alt="JABAWS welcome screen" width="735"
 238                                                 height="461" /></p>
 239                                 <p class="justify">
 240                                         If you need to configure a static IP address the configuration console will
 241                                         help you with this. Shutting down the VM is best from the configuration console as well.
 242                                 </p>
 243
 244                                 <p class="text-right">
 245                                         <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 246                                 </p>
 247                         </div>
 248                 </div>
 249         </div>
 250 </div>
 251 <div class="row" id="vmiaccess">
 252         <div class="col-md-12">
 253                 <div class="panel panel-default">
 254                         <div class="panel panel-heading">
 255                                 <h1 class="panel-title">VM Network Settings</h1>
 256                         </div>
 257                         <div class="panel-body">
 258                                 <p class="justify">
 259                                         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,
 260                                         but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect
 261                                         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
 262                                         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
 263                                         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
 264                                         server to do that).
 265                                 </p>
 266                         </div>
 267                 </div>
 268         </div>
 269 </div>
 270
 271 <jsp:include page="template_footer.jsp" />