website/getting_started.jsp

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   9
  10 <c:import url="template_header.jsp" >
  11     <c:param name="title">Getting Started</c:param>
  12 </c:import>
  13
  14 <div class="row">
  15     <div class="col-md-12">
  16         <div class="panel panel-default">
  17             <div class="panel panel-heading">
  18                 <h1 class="panel-title">JABAWS distributions</h1>
  19             </div>
  20             <div class="panel-body">
  21                 <p class="justify">
  22                     Choose the JABAWS distribution that better suits your needs and read the <em>Getting Started</em> guides below.
  23                     Detailed information is available in the <a href="${pageContext.request.contextPath}/docs/index.html">
  24                     documentation pages</a>.
  25                 </p>
  26                 <br>
  27                 <div class="row">
  28                     <!--<div class="col-md-1"></div>-->
  29                     <div class="col-md-10">
  30                         <table class="table">
  31                             <tr>
  32                                 <th>Quick Guide</th>
  33                                 <th>I want to use JABAWS for...</th>
  34                             </tr>
  35                             <tr>
  36                                 <td><a href="#jalview">Jalview and the JABAWS Public Server</a></td>
  37                                 <td>Running JABAWS services through Jalview on the JABAWS
  38                                     <strong>public</strong> server</td>
  39                             </tr>
  40                             <tr>
  41                                 <td><a href="#client">Command Line Interface (CLI)</a></td>
  42                                 <td>Accessing a <strong>public</strong> or <strong>private</strong>
  43                                     JABAWS server from my own software</td>
  44                             </tr>
  45                             <tr>
  46                                 <td><a href="#war">Web Application aRchive (WAR)</a></td>
  47                                 <td>Running JABAWS for my group, lab, or organization on the
  48                                     <strong>local</strong> infrastructure</td>
  49                             </tr>
  50                             <tr>
  51                                 <td><a href="#va">Virtual Appliance (VA)</a></td>
  52                                 <td>Running JABAWS services through Jalview on my
  53                                     computer with a <strong>private</strong> server</td>
  54                             </tr>
  55
  56                         </table>
  57                     </div>
  58                     <div class="col-md-2"></div>
  59                 </div>
  60             </div>
  61         </div>
  62     </div>
  63 </div>
  64 <div class="row" id="jalview">
  65     <div class="col-md-12">
  66         <div class="panel panel-default">
  67             <div class="panel panel-heading">
  68                 <h1 class="panel-title">Jalview and the JABAWS Public Server</h1>
  69             </div>
  70             <div class="panel-body">
  71                 <!--<h4>Running JABAWS on your local machine</h4>-->
  72
  73                 <p class="justify">
  74                     This is the easiest way to run JABAWS web-services. Simply launch
  75                     <a href="http://www.jalview.org/webstart/jalview.jnlp">Jalview</a> and run any of the methods
  76                     provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default.
  77                     If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can
  78                     either setup a local <a href="#va">JABAWS Virtual Appliance (VA)</a> or
  79                     configue the <a href="#war">JABAWS Web Application aRchive (WAR)</a> in your infrastructure.
  80                 </p>
  81             </div>
  82         </div>
  83     </div>
  84 </div>
  85 <div class="row" id="client">
  86     <div class="col-md-12">
  87         <div class="panel panel-default">
  88             <div class="panel panel-heading">
  89                 <h1 class="panel-title">Command Line Interface (CLI)</h1>
  90             </div>
  91             <div class="panel-body">
  92                 <p class="justify">
  93                     This is a single Java archive which contains the JABAWS command line interface (CLI) client.
  94                     It allows anyone who wants to connect to the JABAWS web-services running at the
  95                     University of Dundee's Public Server, or to run a local private JABAWS server from their own software.
  96                     You can read more about how to use JABAWS command line (CLI) client given in the
  97                     <a href="docs/client.html">documentation pages</a>,
  98                     but a brief instructions are given below:
  99                 </p>
 100                 <ol>
 101                     <li>Download <a href="${pageContext.request.contextPath}/download.jsp#client">the Client Jar file</a></li>
 102                     <li>Download and install <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html">Java</a>
 103                         (version 1.7)</li>
 104                     <li>Provided that you have the Java ready to run, you can get command line help by changing to
 105                         the directory where you downloaded the client jar, and typing:<br/>
 106                         <pre><code class="bash">java -jar jaba-client.jar</code></pre>
 107                     </li>
 108                 </ol>
 109                 <p class="justify">
 110                     The JABA Web Services are WS-I compliant. This means that you can access them from any
 111                     language that has libraries or functions for consuming interoperable SOAP web services.
 112                     More information on how to develop software that access JABAWS services is provided in the
 113                     <a href="docs/develop.html#accessing-jabaws-from-your-program">documentation pages</a>.
 114                     <!-- TODO Provide list of libraries for different languages -->
 115                 </p>
 116                 <p class="text-right">
 117                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 118                 </p>
 119             </div>
 120         </div>
 121     </div>
 122 </div>
 123 <div class="row" id="war">
 124     <div class="col-md-12">
 125         <div class="panel panel-default">
 126             <div class="panel panel-heading">
 127                 <h1 class="panel-title">Web Application aRchive (WAR)</h1>
 128             </div>
 129             <div class="panel-body">
 130
 131                 <!--<h4>Installing a JABAWS Server Web Application Archive (WAR) package</h4>-->
 132                 <p class="justify">
 133                     The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization,
 134                     or wants to enable their local JABAWS server to use the cluster or perform very large tasks.
 135                     Complete documentation is provided in the
 136                     <a href="docs/war.html">documentation pages</a>, but brief instructions are given below:
 137                 </p>
 138                 <ol>
 139                     <li>Download the <a href="${pageContext.request.contextPath}/download.jsp#war">JABAWS WAR file</a></li>
 140                     <li>Download and install <a href="http://tomcat.apache.org/download-80.cgi">Apache-Tomcat</a><br/>
 141                         <em>You will need at least Tomcat version 5.5 of
 142                             (we would recommend version 8.5) and at least Java 1.7 (i.e. JAVA 7).</em>
 143                     </li>
 144                     <li>Drop the JABAWS WAR file into <em2>tomcat/webapps</em2> directory.</li>
 145                     <li>(Re)start the Tomcat.</li>
 146                     <li>Once the tomcat has started, it should automatically unpack the WAR
 147                         into the webapps directory (if it doesn't, simply unpack the WAR archive).</li>
 148                     <li> If you are on Mac or other unix-like architecture with GNU compilers
 149                         available or you'd like to get a maximum performance <br/>
 150                         <em2>cd</em2> to
 151                         <em2>webapps/jabaws/binaries/src/</em2>
 152                         and execute <em2>./compilebin.sh</em2>
 153                         script to compile all binaries JABAWS depends on.
 154                     </li>
 155                 </ol>
 156
 157                 <p><strong>Testing</strong></p>
 158                 <p class="justify">
 159                     You can test that your JABAWS server is working in several ways.
 160                 </p>
 161                 <ol>
 162                     <li>Visit Services Status page available from the JABAWS main page using your web browser.</li>
 163
 164                     <li>If you are working on the command line, then use the command line client shipped with the
 165                         JABAWS war to test it by running:
 166                         <pre><code class="bash">java -jar &lt;Path to tomcat WebApp directory&gt;/jabaws/WEB-INF/lib/jabaws-client.jar -h=http://localhost:8080/jabaws</code></pre>
 167                         In this example we assumed that your JABAWS server URL is
 168                         <em2>http://localhost:8080</em2> and JABAWS context path is
 169                         <em2>jabaws</em2>
 170                     </li>
 171                     <li>Alternately, you can point Jalview at your new server:
 172                         <ol>
 173                             <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
 174                             <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option),
 175                                 elect the <em2>Webservices</em2> panel and press
 176                                 the <em2>New Service URL</em2> button.</li>
 177                             <li>Enter the URL for the tomcat server, including the context path for the
 178                                 JABAWS web app (e.g. http://localhost:8080/jabaws).</li>
 179                         </ol>
 180                     </li>
 181                 </ol>
 182                 <p class="text-right">
 183                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 184                 </p>
 185             </div>
 186         </div>
 187     </div>
 188 </div>
 189 <div class="row" id="va">
 190     <div class="col-md-12">
 191         <div class="panel panel-default">
 192             <div class="panel panel-heading">
 193                 <h1 class="panel-title">Virtual Appliance (VA)</h1>
 194             </div>
 195             <div class="panel-body">
 196                 <!--<h4>Running JABAWS on your local machine</h4>-->
 197
 198                 <p class="justify">
 199                     The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a
 200                     virtual machine on your laptop or desktop computer. A complete guide
 201                     to the JABAWS VA is given in the <a href="${pageContext.request.contextPath}/docs/va.html">documentation pages</a>,
 202                     but for the impatient, brief instructions are given below:
 203                 </p>
 204
 205                 <p class="justify">
 206                     If you work on Windows, Linux or Unix:
 207                 </p>
 208                 <ol>
 209                     <li>Download <a href="${pageContext.request.contextPath}/download.jsp#va">JABAWS Virtual Appliance</a></li>
 210                     <li>Download and install <a href="http://www.vmware.com/products/player">VMWare Player</a></li>
 211                     <li>Unpack the JABAWS virtual appliance and open it with VMware Player</li>
 212                 </ol>
 213
 214                 <p class="justify">
 215                     If you work on Mac do the same using
 216                     <a href="http://www.vmware.com/products/fusion/overview.html">
 217                         VMware Fusion</a>.
 218                 </p>
 219
 220                 <p><strong>Testing</strong></p>
 221                 <p class="justify">
 222                     To check that your JABAWS virtual appliance is working visit the Services Status
 223                     page available from the main JABAWS menu. For this enter the JABAWS URL for your
 224                     new server into a web browser. This is shown once the appliance is booted up.
 225                 </p>
 226                 <p class="justify">
 227                     Alternatively you can use Jalview to complete the testing.
 228                 </p>
 229                 <ol>
 230                     <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
 231                     <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option), select the
 232                         <em2>Webservices</em2> panel and press the
 233                         <em2>New Service URL</em2> button.</li>
 234                     <li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>
 235                 </ol>
 236             </div>
 237         </div>
 238     </div>
 239 </div>
 240
 241 <jsp:include page="template_footer.jsp" />