website/getting_started.jsp

   1 <%--<?xml version="1.0" encoding="ISO-8859-1" ?>--%>
   2 <%--<%@ page language="java" contentType="text/html; charset=ISO-8859-1" pageEncoding="ISO-8859-1"%>--%>
   3
   4 <%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
   5 <%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
   6 <%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
   7 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
   8
   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">Choose a JABAWS distribution</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">JABAWS docs pages</a>.
  24                 </p>
  25                 <br>
  26                 <div class="row">
  27                     <!--<div class="col-md-1"></div>-->
  28                     <div class="col-md-10">
  29                         <table class="table">
  30                             <tr>
  31                                 <th>Quick Guide</th>
  32                                 <th>I want to use JABAWS for...</th>
  33                             </tr>
  34                             <tr>
  35                                 <td><a href="#va">JABAWS Virtual Appliance (VA)</a></td>
  36                                 <td>Running Multiple Sequence Alignments through Jalview on my
  37                                     <strong>own</strong> computer</td>
  38                             </tr>
  39                             <tr>
  40                                 <td><a href="#war">JABAWS Web Application aRchive (WAR)</a></td>
  41                                 <td>Running JABAWS for my group, lab, or organization on the
  42                                     <strong>local</strong> infrastructure </td>
  43                             </tr>
  44                             <tr>
  45                                 <td><a href="#client">JABAWS Java Client</a></td>
  46                                 <td>Accessing a JABAWS server from my own code</td>
  47                             </tr>
  48                         </table>
  49                     </div>
  50                     <div class="col-md-2"></div>
  51                 </div>
  52             </div>
  53         </div>
  54     </div>
  55 </div>
  56 <div class="row" id="va">
  57     <div class="col-md-12">
  58         <div class="panel panel-default">
  59             <div class="panel panel-heading">
  60                 <h1 class="panel-title">JABAWS Virtual Appliance (VA)</h1>
  61             </div>
  62             <div class="panel-body">
  63                 <!--<h4>Running JABAWS on your local machine</h4>-->
  64
  65                 <p class="justify">
  66                     The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a
  67                     virtual machine on your laptop or desktop computer. A <a href="man_servervm.jsp#whenvm">complete guide
  68                     to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:
  69                 </p>
  70
  71                 <p class="justify">
  72                     If you work on Windows, Linux or Unix:
  73                 </p>
  74                 <ol>
  75                     <li>Download <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">JABAWS Virtual Appliance</a></li>
  76                     <li>Download and install <a href="http://www.vmware.com/products/player">VMWare Player</a>.</li>
  77                     <li>Unpack the JABAWS virtual appliance and open it with VMware Player.</li>
  78                 </ol>
  79
  80                 <p class="justify">
  81                     If you work on Mac do the same using
  82                     <a href="http://www.vmware.com/products/fusion/overview.html">
  83                         VMware Fusion</a>, or for free alternative use a WAR JABAWS package.
  84                 </p>
  85
  86                 <p><strong>Testing</strong></p>
  87                 <p class="justify">
  88                     To check that your JABAWS virtual appliance is working visit the Services Status
  89                     page available from the main JABAWS menu. For this enter the JABAWS URL for your
  90                     new server into a web browser. This is shown once the appliance is booted up.
  91                 </p>
  92                 <p class="justify">
  93                     Alternatively you can use Jalview to complete the testing.
  94                 </p>
  95                 <ol>
  96                     <li>Launch the desktop version of <a href="http://www.jalview.org/download.html">Jalview</a></li>
  97                     <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option), select the
  98                         <em2>Webservices</em2> panel and press the
  99                         <em2>New Service URL</em2> button.</li>
 100                     <li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>
 101                 </ol>
 102             </div>
 103         </div>
 104     </div>
 105 </div>
 106 <div class="row" id="war">
 107     <div class="col-md-12">
 108         <div class="panel panel-default">
 109             <div class="panel panel-heading">
 110                 <h1 class="panel-title">JABAWS Web Application aRchive (WAR)</h1>
 111             </div>
 112             <div class="panel-body">
 113
 114                 <!--<h4>Installing a JABAWS Server Web Application Archive (WAR) package</h4>-->
 115                 <p class="justify">
 116                     This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable
 117                     their local JABA server to use the cluster or perform very large tasks.
 118                 </p>
 119                 <ol>
 120                     <li>Download the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">JABAWS WAR file</a></li>
 121                     <li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a>.<br/>
 122                         <em2>You will need at least Tomcat version 5.5 of
 123                             (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).</em2>
 124                     </li>
 125                     <li>Drop the JABAWS WAR file into <em2>tomcat/webapps</em2> directory.</li>
 126                     <li>(Re)start the Tomcat.</li>
 127                     <li>Once the tomcat has started, it should automatically unpack the WAR
 128                         into the webapps directory (if it doesn't, then you'll need to do this
 129                         manually, it's just a zip archive in the end).</li>
 130                     <li> If you are on Mac or other unix-like architecture with GNU compilers
 131                         available or you'd like to get a maximum performance <br/>
 132                         <em2>cd</em2> to
 133                         <em2>webapps/jabaws/binaries/src/</em2>
 134                         and execute <em2>./compilebin.sh</em2>
 135                         script to compile all binaries JABAWS depends on.
 136                     </li>
 137                 </ol>
 138
 139                 <p><strong>Testing</strong></p>
 140                 <p class="justify">
 141                     You can test that your JABAWS server is working in several ways.
 142                 </p>
 143                 <ol>
 144                     <li>Visit Services Status page available from the JABAWS main page using your web browser.</li>
 145
 146                     <li>If you are working on the command line, then use the command line client shipped with the
 147                         JABAWS war to test it by running:
 148                         <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>
 149                         In this example we assumed that your JABAWS server URL is
 150                         <em2>http://localhost:8080</em2> and JABAWS context path is
 151                         <em2>jabaws</em2>
 152                     </li>
 153                     <li>Alternately, you can point Jalview at your new server:
 154                         <ul>
 155                             <li>Launch the desktop version of <a href="http://www.jalview.org/download.html">Jalview</a></li>
 156                             <li>Open the Jalview desktop's preferences panel (from the Tools-&gt;Preferences menu option),
 157                                 elect the <em2>Webservices</em2> panel and press
 158                                 the <em2>New Service URL</em2> button.</li>
 159                             <li>Enter the URL for the tomcat server, including the context path for the
 160                                 JABAWS web app (e.g. http://localhost:8080/jabaws).</li>
 161                         </ul>
 162                     </li>
 163                 </ol>
 164             </div>
 165         </div>
 166     </div>
 167 </div>
 168 <div class="row" id="client">
 169     <div class="col-md-12">
 170         <div class="panel panel-default">
 171             <div class="panel panel-heading">
 172                 <h1 class="panel-title">JABAWS Command Line Java Client</h1>
 173             </div>
 174             <div class="panel-body">
 175                 <p class="justify">
 176                     This is a single java archive which contains the JABAWS command line client. It requires Java
 177                     version 1.6 to run, and allows anyone who wants to connect to and to use JABAWS from their own
 178                     software.
 179                 </p>
 180                 <ol>
 181                     <li>Download <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">the Client Jar file</a></li>
 182                 </ol>
 183                 <p class="justify">
 184                     You can read more about how to use command line client <a href="man_client.jsp">in
 185                     the CMD Client</a> section of the manual. You can also get command line help by changing to
 186                     the directory where you downloaded the client jar, and typing:
 187                 </p>
 188                 <pre><code class="bash">java -jar jaba-client.jar</code></pre>
 189                 <p class="justify">
 190                     A JABA Web Services are WS-I compliant. This means that you can access them from any
 191                     language that has libraries or functions for consuming interoperable SOAP web services.
 192                     <!-- TODO Provide list of libraries for different languages -->
 193                 </p>
 194             </div>
 195         </div>
 196     </div>
 197 </div>
 198
 199 <jsp:include page="template_footer.jsp" />