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+\r
<head>\r
-<meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
+<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started</title>\r
-<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
-<link rel="stylesheet" type="text/css" media="print" href="print.css"/>\r
-\r
+<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
+<link href="print.css" rel="stylesheet" type="text/css" media="print" />\r
+<link href='http://fonts.googleapis.com/css?family=Yanone+Kaffeesatz:700' rel='stylesheet' type='text/css' />\r
<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
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+\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\r
-<table> \r
+<table>\r
<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/jabaws21.png" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
\r
<div id="wrapper">\r
<div id="panel">\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="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
+ <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-1.cluster.lifesci.dundee.ac.uk:8086/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="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a class="newa" href="jabaws_funding.html">Funding</a>\r
+</div>\r
+<!-- panel end-->\r
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-</div><!-- panel end-->\r
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<div id="content">\r
-\r
<h2 id="headtitle">Getting Started</h2>\r
-\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
-\r
<table id="choicematrix">\r
<tr>\r
<th>I want to use JABAWS for...</th>\r
<th>Quick Guide</th>\r
</tr>\r
<tr>\r
- <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
- <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
</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 on the Amazon cloud </a></td>\r
+ <td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
+ <td><a href="manual_qs_amazon.html#qsc">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
- <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
</tr>\r
<tr>\r
- <td>Accessing a JABAWS server from my own code</td>\r
- <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
</tr>\r
</table>\r
\r
-<a name="qsc"/>\r
\r
+<a name="qsc"/>\r
<h3>Installing A JABAWS Server Web Application Archive (WAR) package</h3>\r
-\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
+<p>\r
+ This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable \r
+ their local JABA server to use the cluster or perform very large tasks.\r
+</p>\r
\r
<ol>\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> 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
+ <li>Download the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/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
+ <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> If you are on Mac or other unix-like architecture with GNU compilers available or you'd like to get a maximum performance <br/>\r
+ <span class="hightlight">cd</span> to <span class="hightlight">webapps/jabaws/binaries/src/</span> \r
+ and execute <span class="hightlight">./compilebin.sh</span> script to compile all binaries JABAWS depends on.\r
+ </li>\r
</ol> \r
\r
<h3>Testing</h3>\r
\r
<!-- TODO put JABAWS CMD test instructions here -->\r
</div> <!-- content end-->\r
-<!-- about end-->\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
-\r
+<div id="copyright">Last update: 14 October 2013<br/>Sasha Sherstnev, 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