<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">Choose a JABAWS distribution</h1>
+ <h1 class="panel-title">JABAWS distributions</h1>
</div>
<div class="panel-body">
<p class="justify">
Choose the JABAWS distribution that better suits your needs and read the quickstart guides below.
- Detailed information is available in the <a href="${pageContext.request.contextPath}/man_docs.jsp">JABAWS docs pages</a>.
+ Detailed information is available in the <a href="${pageContext.request.contextPath}/man_docs.jsp">
+ JABAWS documentation pages</a>.
</p>
<br>
<div class="row">
<th>I want to use JABAWS for...</th>
</tr>
<tr>
+ <td><a href="#jalview">Jalview and the JABAWS Public Server</a></td>
+ <td>Running JABAWS services through Jalview on the JABAWS
+ <strong>public</strong> server</td>
+ </tr>
+ <tr>
<td><a href="#va">JABAWS Virtual Appliance (VA)</a></td>
- <td>Running Multiple Sequence Alignments through Jalview on my
- <strong>own</strong> computer</td>
+ <td>Running JABAWS services through Jalview on my
+ computer with a <strong>private</strong> server</td>
</tr>
<tr>
<td><a href="#war">JABAWS Web Application aRchive (WAR)</a></td>
<td>Running JABAWS for my group, lab, or organization on the
- <strong>local</strong> infrastructure </td>
+ <strong>local</strong> infrastructure</td>
</tr>
<tr>
- <td><a href="#client">JABAWS Java Client</a></td>
- <td>Accessing a JABAWS server from my own code</td>
+ <td><a href="#client">JABAWS Command Line Interface (CLI)</a></td>
+ <td>Accessing a <strong>public</strong> or <strong>private</strong>
+ JABAWS server from my own software</td>
</tr>
</table>
</div>
</div>
</div>
</div>
+<div class="row" id="jalview">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">Jalview and the JABAWS Public Server</h1>
+ </div>
+ <div class="panel-body">
+ <!--<h4>Running JABAWS on your local machine</h4>-->
+
+ <p class="justify">
+ This is the easiest way to run JABAWS web-services. Simply launch
+ <a href="http://www.jalview.org/webstart/jalview.jnlp">Jalview</a> and run any of the methods
+ provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default.
+ If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can
+ either setup a local <a href="#va">JABAWS Virtual Appliance (VA)</a> or
+ configue the <a href="#war">JABAWS Web Application aRchive (WAR)</a> in your infrastructure.
+ </p>
+ </div>
+ </div>
+ </div>
+</div>
<div class="row" id="va">
<div class="col-md-12">
<div class="panel panel-default">
<p class="justify">
The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a
- virtual machine on your laptop or desktop computer. A <a href="man_servervm.jsp#whenvm">complete guide
- to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:
+ virtual machine on your laptop or desktop computer. A complete guide
+ to the JABAWS VA is given in the <a href="${pageContext.request.contextPath}/man_servervm.jsp">documentation pages</a>,
+ but for the impatient, brief instructions are given below:
</p>
<p class="justify">
If you work on Windows, Linux or Unix:
</p>
<ol>
- <li>Download <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">JABAWS Virtual Appliance</a></li>
- <li>Download and install <a href="http://www.vmware.com/products/player">VMWare Player</a>.</li>
- <li>Unpack the JABAWS virtual appliance and open it with VMware Player.</li>
+ <li>Download <a href="${pageContext.request.contextPath}/download.jsp#va">JABAWS Virtual Appliance</a></li>
+ <li>Download and install <a href="http://www.vmware.com/products/player">VMWare Player</a></li>
+ <li>Unpack the JABAWS virtual appliance and open it with VMware Player</li>
</ol>
<p class="justify">
If you work on Mac do the same using
<a href="http://www.vmware.com/products/fusion/overview.html">
- VMware Fusion</a>, or for free alternative use a WAR JABAWS package.
+ VMware Fusion</a>.
</p>
<p><strong>Testing</strong></p>
Alternatively you can use Jalview to complete the testing.
</p>
<ol>
- <li>Launch the desktop version of <a href="http://www.jalview.org/download.html">Jalview</a></li>
+ <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
<li>Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the
<em2>Webservices</em2> panel and press the
<em2>New Service URL</em2> button.</li>
<li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>
</ol>
+ <p class="text-right">
+ <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
+ </p>
</div>
</div>
</div>
<!--<h4>Installing a JABAWS Server Web Application Archive (WAR) package</h4>-->
<p class="justify">
- This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable
- their local JABA server to use the cluster or perform very large tasks.
+ The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization,
+ or wants to enable their local JABAWS server to use the cluster or perform very large tasks.
+ Complete documentation is provided in the
+ <a href="man_serverwar.jsp">documentation pages</a>, but brief instructions are given below:
</p>
<ol>
- <li>Download the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">JABAWS WAR file</a></li>
- <li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a>.<br/>
- <em2>You will need at least Tomcat version 5.5 of
- (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).</em2>
+ <li>Download the <a href="${pageContext.request.contextPath}/download.jsp#war">JABAWS WAR file</a></li>
+ <li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a><br/>
+ <em>You will need at least Tomcat version 5.5 of
+ (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).</em>
</li>
<li>Drop the JABAWS WAR file into <em2>tomcat/webapps</em2> directory.</li>
<li>(Re)start the Tomcat.</li>
<li>Once the tomcat has started, it should automatically unpack the WAR
- into the webapps directory (if it doesn't, then you'll need to do this
- manually, it's just a zip archive in the end).</li>
+ into the webapps directory (if it doesn't, simply unpack the WAR archive).</li>
<li> If you are on Mac or other unix-like architecture with GNU compilers
available or you'd like to get a maximum performance <br/>
<em2>cd</em2> to
<em2>jabaws</em2>
</li>
<li>Alternately, you can point Jalview at your new server:
- <ul>
- <li>Launch the desktop version of <a href="http://www.jalview.org/download.html">Jalview</a></li>
+ <ol>
+ <li>Launch the desktop version of <a href="http://www.jalview.org/">Jalview</a></li>
<li>Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option),
elect the <em2>Webservices</em2> panel and press
the <em2>New Service URL</em2> button.</li>
<li>Enter the URL for the tomcat server, including the context path for the
JABAWS web app (e.g. http://localhost:8080/jabaws).</li>
- </ul>
+ </ol>
</li>
</ol>
+ <p class="text-right">
+ <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
+ </p>
</div>
</div>
</div>
</div>
<div class="panel-body">
<p class="justify">
- This is a single java archive which contains the JABAWS command line client. It requires Java
- version 1.6 to run, and allows anyone who wants to connect to and to use JABAWS from their own
- software.
+ This is a single Java archive which contains the JABAWS command line interface (CLI) client.
+ It allows anyone who wants to connect to the JABAWS web-services running at the
+ University of Dundee's Public Server, or to run a local private JABAWS server from their own software.
+ You can read more about how to use JABAWS command line (CLI) client given in the
+ <a href="man_client.jsp">documentation pages</a>,
+ but a brief instructions are given below:
</p>
<ol>
- <li>Download <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">the Client Jar file</a></li>
+ <li>Download <a href="${pageContext.request.contextPath}/download.jsp#client">the Client Jar file</a></li>
+ <li>Download and install <a href="http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase6-419409.html">Java</a>
+ (version 1.6)</li>
+ <li>Provided that you have the Java ready to run, you can get command line help by changing to
+ the directory where you downloaded the client jar, and typing:<br/>
+ <pre><code class="bash">java -jar jaba-client.jar</code></pre>
+ </li>
</ol>
<p class="justify">
- You can read more about how to use command line client <a href="man_client.jsp">in
- the CMD Client</a> section of the manual. You can also get command line help by changing to
- the directory where you downloaded the client jar, and typing:
- </p>
- <pre><code class="bash">java -jar jaba-client.jar</code></pre>
- <p class="justify">
- A JABA Web Services are WS-I compliant. This means that you can access them from any
+ The JABA Web Services are WS-I compliant. This means that you can access them from any
language that has libraries or functions for consuming interoperable SOAP web services.
<!-- TODO Provide list of libraries for different languages -->
</p>
git://source.jalview.org / jabaws.git / commitdiff