<a class="newa" href="index.html">Home</a> \r
<a class="newa" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newpressed" href="contacts.html">Contact Us</a>\r
<a class="newpressed" href="index.html">Home</a> \r
<a class="newa" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
<div class="brick">\r
<div class="brick_header"><h2>For Users</h2></div>\r
<div class="brick_content">\r
- <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download//get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)\r
or <a href="man_awscloud.html">JABAWS on Amazon Webservices Cloud</a><br/>\r
<strong>The Main Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
<p>To use JABAWS web services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
<p>\r
- <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web \r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web \r
Application aRchive</a> (55M)\r
</p>\r
<p>JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>\r
<td><div class="brick">\r
<div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
<div class="brick_content">\r
-<strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
+<strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
<br/>\r
<strong>The Client: </strong>\r
- Command Line Client <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
-"http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jaba-client-src-2.1.jar">source</a> \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.1.jar">source</a> \r
\r
<p>\r
You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. \r
</div>\r
\r
<h3 style="margin:0;">Public JABAWS Server</h3>\r
-<p> You can access our public JABAWS web services with our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">command line client</a>, \r
+<p> You can access our public JABAWS web services with our <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.1.jar">command line client</a>, \r
<a href="http://www.jalview.org/download.html">Jalview</a>, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1.\r
The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
<ul>\r
</ul>\r
<p>These web services accept submissions of <strong>less than one thousand sequences</strong>. Should you find this to be insufficient for your needs, \r
or if you are concerned about privacy or on an unreliable network connection, then you can \r
- <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
\r
\r
\r
<a class="newa" href="index.html">Home</a> \r
<a class="newa" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
<li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
</ul>\r
\r
-All these codes including Jronn and AAcon are available at the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
section (registration is required).\r
\r
\r
JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home \r
page, and you can use this to automatically generate service bindings for your program. If you use Java \r
- you may wish to use our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">client package</a> to access JABAWS. \r
+ you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. \r
This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify \r
working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
\r
<h2><a name="usingcclient" id="usingcclient"></a>JABAWS Command Line Client Usage </h2>\r
<p>\r
-The command line client comes as a part of <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download"> client package</a> which you are welcome to download. \r
+The command line client comes as a part of <a href="http://www.compbio.dundee.ac.uk/download"> client package</a> which you are welcome to download. \r
The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of \r
the functions which can be accessed programmatically via <a href="dm_javadoc/index.html">JABAWS API</a>. Using this client you could align sequences \r
using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.\r
<h3><a name="connectto" id="connectto"></a>Connecting to JABAWS</h3>\r
<p class="attention">\r
For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client \r
-<<<<<<< HEAD\r
-source code is available from the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">download page</a>. Please note that for now all \r
+source code is available from the <a href="http://www.compbio.dundee.ac.uk/download">download page</a>. Please note that for now all \r
the examples are in Java other languages will follow given a sufficient demand. </p>\r
-=======\r
-source code is available from the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">download page</a>. Please note that for now all \r
-the examples are in Java, other languages will follow if there is sufficient demand. </p>\r
->>>>>>> 42a3637e24a7a65b5a1e6048e581df998b4a4f95\r
+\r
<p>\r
Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal \r
web service deployed in the University of Dundee. </p>\r
this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, \r
the alternatives given in the code are line commented // comment. You may want to remove line style comments to \r
test alternatives of the functions. All you need for this to work is a \r
-<a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.0.jar">JABAWS binary client</a>. \r
+<a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">JABAWS binary client</a>. \r
Please make sure that the client is in the Java class path before running this example.</p>\r
<pre class="code" style="line-height:1em;">\r
import java.io.ByteArrayInputStream;\r
<a class="newa" href="index.html">Home</a> \r
<a class="newpressed" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
<a class="newa" href="index.html">Home</a> \r
<a class="newpressed" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
\r
<a name="qsc"/>\r
<h3><a name="client"/>The JABAWS command line client</h3>\r
-<ul><li>Download <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">the Client Jar file</a></li>\r
+<ul><li>Download <a href="http://www.compbio.dundee.ac.uk/download">the Client Jar file</a></li>\r
</ul>\r
<p>\r
This is a single java archive which contains the JABAWS command line client. It requires Java \r
<a class="newa" href="index.html">Home</a> \r
<a class="newpressed" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
\r
<a name="qsc"/>\r
<h3>Running JABAWS on your local machine</h3>\r
-<ul><li>Download <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">JABAWS Virtual Appliance</a></li>\r
+<ul><li>Download <a href="http://www.compbio.dundee.ac.uk/download">JABAWS Virtual Appliance</a></li>\r
</ul>\r
<p>\r
The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a \r
<a class="newa" href="index.html">Home</a> \r
<a class="newpressed" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
</p>\r
\r
<ol>\r
- <li>Download the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">JABAWS WAR file</a></li>\r
+ <li>Download the <a href="http://www.compbio.dundee.ac.uk/download">JABAWS WAR file</a></li>\r
<li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a>.<br/>\r
<span class="hightlight">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).</span>\r
</li>\r
<a class="newa" href="index.html">Home</a> \r
<a class="newpressed" href="quick_start.html">Getting Started</a> \r
<a class="newa" href="man_about.html">Manual</a> \r
- <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
<a class="newa" href="contacts.html">Contact Us</a>\r
git://source.jalview.org / jabaws.git / commitdiff