website/getting_started.jsp

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  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 quickstart guides below.
  23                     Detailed information is available in the <a href="${pageContext.request.contextPath}/man_docs.jsp">
  24                     JABAWS 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="#va">JABAWS Virtual Appliance (VA)</a></td>
  42                                 <td>Running JABAWS services through Jalview on my
  43                                     computer with a <strong>private</strong> server</td>
  44                             </tr>
  45                             <tr>
  46                                 <td><a href="#war">JABAWS 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="#client">JABAWS Command Line Interface (CLI)</a></td>
  52                                 <td>Accessing a <strong>public</strong> or <strong>private</strong>
  53                                     JABAWS server from my own software</td>
  54                             </tr>
  55                         </table>
  56                     </div>
  57                     <div class="col-md-2"></div>
  58                 </div>
  59             </div>
  60         </div>
  61     </div>
  62 </div>
  63 <div class="row" id="jalview">
  64     <div class="col-md-12">
  65         <div class="panel panel-default">
  66             <div class="panel panel-heading">
  67                 <h1 class="panel-title">Jalview and the JABAWS Public Server</h1>
  68             </div>
  69             <div class="panel-body">
  70                 <!--<h4>Running JABAWS on your local machine</h4>-->
  71
  72                 <p class="justify">
  73                     This is the easiest way to run JABAWS web-services. Simply launch
  74                     <a href="http://www.jalview.org/webstart/jalview.jnlp">Jalview</a> and run any of the methods
  75                     provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default.
  76                     If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can
  77                     either setup a local <a href="#va">JABAWS Virtual Appliance (VA)</a> or
  78                     configue the <a href="#war">JABAWS Web Application aRchive (WAR)</a> in your infrastructure.
  79                 </p>
  80             </div>
  81         </div>
  82     </div>
  83 </div>
  84 <div class="row" id="va">
  85     <div class="col-md-12">
  86         <div class="panel panel-default">
  87             <div class="panel panel-heading">
  88                 <h1 class="panel-title">JABAWS Virtual Appliance (VA)</h1>
  89             </div>
  90             <div class="panel-body">
  91                 <!--<h4>Running JABAWS on your local machine</h4>-->
  92
  93                 <p class="justify">
  94                     The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a
  95                     virtual machine on your laptop or desktop computer. A complete guide
  96                     to the JABAWS VA is given in the <a href="${pageContext.request.contextPath}/man_servervm.jsp">documentation pages</a>,
  97                     but for the impatient, brief instructions are given below:
  98                 </p>
  99
 100                 <p class="justify">
 101                     If you work on Windows, Linux or Unix:
 102                 </p>
 103                 <ol>
 104                     <li>Download <a href="${pageContext.request.contextPath}/download.jsp#va">JABAWS Virtual Appliance</a></li>
 105                     <li>Download and install <a href="http://www.vmware.com/products/player">VMWare Player</a></li>
 106                     <li>Unpack the JABAWS virtual appliance and open it with VMware Player</li>
 107                 </ol>
 108
 109                 <p class="justify">
 110                     If you work on Mac do the same using
 111                     <a href="http://www.vmware.com/products/fusion/overview.html">
 112                         VMware Fusion</a>.
 113                 </p>
 114
 115                 <p><strong>Testing</strong></p>
 116                 <p class="justify">
 117                     To check that your JABAWS virtual appliance is working visit the Services Status
 118                     page available from the main JABAWS menu. For this enter the JABAWS URL for your
 119                     new server into a web browser. This is shown once the appliance is booted up.
 120                 </p>
 121                 <p class="justify">
 122                     Alternatively you can use Jalview to complete the testing.
 123                 </p>
 124                 <ol>
 125                     <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
 126                     <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option), select the
 127                         <em2>Webservices</em2> panel and press the
 128                         <em2>New Service URL</em2> button.</li>
 129                     <li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>
 130                 </ol>
 131                 <p class="text-right">
 132                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 133                 </p>
 134             </div>
 135         </div>
 136     </div>
 137 </div>
 138 <div class="row" id="war">
 139     <div class="col-md-12">
 140         <div class="panel panel-default">
 141             <div class="panel panel-heading">
 142                 <h1 class="panel-title">JABAWS Web Application aRchive (WAR)</h1>
 143             </div>
 144             <div class="panel-body">
 145
 146                 <!--<h4>Installing a JABAWS Server Web Application Archive (WAR) package</h4>-->
 147                 <p class="justify">
 148                     The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization,
 149                     or wants to enable their local JABAWS server to use the cluster or perform very large tasks.
 150                     Complete documentation is provided in the
 151                     <a href="man_serverwar.jsp">documentation pages</a>, but brief instructions are given below:
 152                 </p>
 153                 <ol>
 154                     <li>Download the <a href="${pageContext.request.contextPath}/download.jsp#war">JABAWS WAR file</a></li>
 155                     <li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a><br/>
 156                         <em>You will need at least Tomcat version 5.5 of
 157                             (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).</em>
 158                     </li>
 159                     <li>Drop the JABAWS WAR file into <em2>tomcat/webapps</em2> directory.</li>
 160                     <li>(Re)start the Tomcat.</li>
 161                     <li>Once the tomcat has started, it should automatically unpack the WAR
 162                         into the webapps directory (if it doesn't, simply unpack the WAR archive).</li>
 163                     <li> If you are on Mac or other unix-like architecture with GNU compilers
 164                         available or you'd like to get a maximum performance <br/>
 165                         <em2>cd</em2> to
 166                         <em2>webapps/jabaws/binaries/src/</em2>
 167                         and execute <em2>./compilebin.sh</em2>
 168                         script to compile all binaries JABAWS depends on.
 169                     </li>
 170                 </ol>
 171
 172                 <p><strong>Testing</strong></p>
 173                 <p class="justify">
 174                     You can test that your JABAWS server is working in several ways.
 175                 </p>
 176                 <ol>
 177                     <li>Visit Services Status page available from the JABAWS main page using your web browser.</li>
 178
 179                     <li>If you are working on the command line, then use the command line client shipped with the
 180                         JABAWS war to test it by running:
 181                         <pre><code class="bash">java -jar &lt;Path to tomcat WebApp directory&gt;/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws</code></pre>
 182                         In this example we assumed that your JABAWS server URL is
 183                         <em2>http://localhost:8080</em2> and JABAWS context path is
 184                         <em2>jabaws</em2>
 185                     </li>
 186                     <li>Alternately, you can point Jalview at your new server:
 187                         <ol>
 188                             <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
 189                             <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option),
 190                                 elect the <em2>Webservices</em2> panel and press
 191                                 the <em2>New Service URL</em2> button.</li>
 192                             <li>Enter the URL for the tomcat server, including the context path for the
 193                                 JABAWS web app (e.g. http://localhost:8080/jabaws).</li>
 194                         </ol>
 195                     </li>
 196                 </ol>
 197                 <p class="text-right">
 198                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
 199                 </p>
 200             </div>
 201         </div>
 202     </div>
 203 </div>
 204 <div class="row" id="client">
 205     <div class="col-md-12">
 206         <div class="panel panel-default">
 207             <div class="panel panel-heading">
 208                 <h1 class="panel-title">JABAWS Command Line Java Client</h1>
 209             </div>
 210             <div class="panel-body">
 211                 <p class="justify">
 212                     This is a single Java archive which contains the JABAWS command line interface (CLI) client.
 213                     It allows anyone who wants to connect to the JABAWS web-services running at the
 214                     University of Dundee's Public Server, or to run a local private JABAWS server from their own software.
 215                     You can read more about how to use JABAWS command line (CLI) client given in the
 216                     <a href="man_client.jsp">documentation pages</a>,
 217                     but a brief instructions are given below:
 218                 </p>
 219                 <ol>
 220                     <li>Download <a href="${pageContext.request.contextPath}/download.jsp#client">the Client Jar file</a></li>
 221                     <li>Download and install <a href="http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase6-419409.html">Java</a>
 222                         (version 1.6)</li>
 223                     <li>Provided that you have the Java ready to run, you can get command line help by changing to
 224                         the directory where you downloaded the client jar, and typing:<br/>
 225                         <pre><code class="bash">java -jar jaba-client.jar</code></pre>
 226                     </li>
 227                 </ol>
 228                 <p class="justify">
 229                     The JABA Web Services are WS-I compliant. This means that you can access them from any
 230                     language that has libraries or functions for consuming interoperable SOAP web services.
 231                     <!-- TODO Provide list of libraries for different languages -->
 232                 </p>
 233             </div>
 234         </div>
 235     </div>
 236 </div>
 237
 238 <jsp:include page="template_footer.jsp" />