<div id="banner">\r
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<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0" title="Java Bioinformatics Analysis Web Services version 2.0"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<a href="index.html">Home</a>\r
<a class="selected" href="quick_start.html">Getting Started</a> \r
<a href="man_about.html">Manual</a> \r
- <a href="download.html">Download</a>\r
- <a href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
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</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="man_awscloud.html">JABAWS AMI</a></td>\r
+ <td><a href="man_awscloud.html">JABAWS on the Amazon cloud </a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
<p>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.</p>\r
\r
<ol>\r
-<li>Download the <a href="http://www.compbio.dundee.ac.uk/jabaws/download.html">JABAWS WAR for your platform </a></li>\r
+<li>Download the <a href="http://www.compbio.dundee.ac.uk/download">JABAWS WAR for your platform </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 version 5.5 of Tomcat (we would recommend version 7.0) and at least version 1.6 (i.e. JAVA 6) of Java.</span></li>\r
<li>Drop the JABAWS WAR file into <span class="hightlight">tomcat/webapps</span> directory.</li>\r
<li>(Re)start the Tomcat.</li>\r
<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>\r
- <li>You then need to complete the installation of the executable binaries:</li>\r
- <ul>\r
- <li>If you are on Linux or Mac (OSX intel Mac only) <br/>\r
- <span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./setexecflag.sh </span> script to ensure the JABAWS binaries can be executed. </li>\r
- <li>If you are on other unix-like architecture with gnu compilers available or you'd like to get a maximum performance:</li>\r
- <li> <span class="hightlight">cd</span> to <span class="hightlight">webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./compilebin.sh </span> script to compile all binaries JABAWS depends on. </li>\r
- <li><span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/ </span>and execute <span class="hightlight">./setexecflag.sh </span> script. </li>\r
- </ul>\r
+ <li> If you are on Mac or other unix-like architecture with GNU compilers available or you'd like to get a maximum performance </li>\r
+ <ul><li> <span class="hightlight">cd</span> to <span class="hightlight">webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./compilebin.sh </span> script to compile all binaries JABAWS depends on. </li>\r
+ </ul>\r
</ol> \r
\r
<h3>Testing</h3>\r
-<p>You can test that your JABAWS server is working in two ways.</p>\r
+<p>You can test that your JABAWS server is working in several ways.</p>\r
<ol>\r
+<li>Visit Services Status page available from the JABAWS main page using your web browser.</li>\r
+\r
<li>If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running:\r
-<span class="code">java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws</span>\r
-In this example we assumed that your JABAWS server URL is <span class="hightlight">http://localhost:8080</span> and JABAWS context path is <span class="hightlight">jabaws</span>\r
+ <span class="code">java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws</span>\r
+ In this example we assumed that your JABAWS server URL is <span class="hightlight">http://localhost:8080</span> and JABAWS context path is <span class="hightlight">jabaws</span>\r
</li>\r
-\r
<li>Alternately, you can point Jalview at your new server:\r
<ul>\r
<li>Launch the desktop version of <a href="http://www.jalview.org/download.html">Jalview</a></li>\r
<!-- TODO put JABAWS CMD test instructions here -->\r
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<!-- about end-->\r
-<div id="copyright">Last update: 10 August 2011<br/>\r
+<div id="copyright">Last update: 16 September 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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git://source.jalview.org / jabaws.git / blobdiff