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<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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- <h4>JABAWS Javadoc</h4>\r
- <p><a href="dm_javadoc/index.html">Data model</a> javadoc- read this if your are coding against JABA Web Services</p>\r
- <p><a href="full_javadoc/index.html">Complete</a> javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly</p>\r
- <h4>Starting up from the source code</h4>\r
-<p><a name="svn">SVN source repository:</a><a href="link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1">https://svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1</a><br/>\r
-The repository contains a complete JABAWS <a href="http://www.eclipse.org">Eclipse</a> project. To use Eclipse with this repository you need to install Eclipse SVN plugin which could be found here: http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA. Eclipse update web site address is <a href="http://subclipse.tigris.org/update_1.4.x">http://subclipse.tigris.org/update_1.4.x</a> Take care to install 1.4.x version of the plugin, as SVN repository will not work with more recent clients. it would help to install TestNG plugin as well which could be downloaded from <a href="http://testng.org/doc/download.html">http://testng.org/doc/download.html</a>. Please note however that no generated code is stored in the repository. That is to say that if you like to obtain client or server packages it is better to download them from the download section of this web site. Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using <span class="hightlight">build-server</span> task from <span class="hightlight">wsbuild.xml</span> ant script, than you could use build.xml tasks to generate any of the distributives you need. </p>\r
-<h4>Structure of the project</h4>\r
-<img style="padding:0 1em;" align="left" src="images/ws-structure.png" alt="JABAWS layers" />\r
-<p>Layers in the source code are defined in a different source folders which are: \r
-<br/><span class="hightlight">/webservices<br />\r
- /runner<br />\r
- /engine<br />\r
- /datamodel</span></p>\r
-<p style="clear:both">JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above.</p>\r
-<p>The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. The code on this level code engine. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above.</p>\r
-<p>The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services.</p>\r
-<p>Finally, the upper layer contains the web services, that depend on all the layers below.</p>\r
-<p>The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation.</p>\r
-<p>A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.</p>\r
-\r
-<h4>Running tests</h4>\r
-<p>The test results for the JABAWS package offered for download can be found here: <a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">Test Results</a><br/>\r
-JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a> for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases. </p>\r
-<p>The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. \r
-Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster.\r
-Several testing groups are supported: \r
-<ul>\r
-<li>All tests (Test)</li>\r
-<li>Cluster tests (Run_cluster_dependent_test)</li>\r
-<li>Cluster independent tests () </li>\r
-<li>Windows only tests (All_cluster_independent_windows_only_tests) </li>\r
-<li>Performance and stability tests (Long_tests) </li>\r
-<li>Re-run failed tests (Rerun_failed_tests) </li>\r
-<li>Run custom test (CustomTest) </li>\r
-</ul>\r
-<p>To run the tests you need to download all sources from <a href="#svn">repository</a>. Once you have done that, enter into the command line mode, change directory to the project directory and type: \r
- <span class="code">ant -f build.xml <test group name></span> </p>\r
- <p>. Make sure you have <a href="http://ant.apache.org/">Apache Ant</a> \r
- installed and path to ant executable is defined in your path environmental variable. \r
- Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests \r
- use the following \r
- command: <span class="code">ant -f build.xml Run_cluster_dependent_test</span>\r
- If you work under Linux you could use a simple script from the root folder of repository called <span class="hightlight">runtests.sh</span> This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse.\r
- </p>\r
- </p>\r
- <p>A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in <span class="hightlight">test-output/testng-failed.xml</span>. and is used in the ant task called <span class="hightlight">Rerun_failed_tests</span>. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: <span class="code">ant -f build.xml Rerun_failed_tests</span> CustomTest runs the test defined in the project root directory file called <span class="hightlight">temp-testng-customsuite.xml</span>. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. </p>\r
- <p class="hightlight">For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.</p>\r
-\r
- <h4>Preparing distributive's</h4>\r
- <p>There are a number of ant tasks aimed for preparing distributives for download.\r
- Currently a few types of JABAWS packages are offered \r
- <ol>\r
- <li>Client only (contains classes required to access JABA Web Services)</li>\r
- <li>Platform specific JABAWS (windows and other)</li>\r
- <li>JABA Web Services without JAXWS libraries ( a the runtime dependency) </li>\r
- <li>JABAWS without binaries</li>\r
- <li>JABAWS without binaries and jax-ws </li>\r
- <li>JABAWS framework </li>\r
- </ol>\r
- </p>\r
- Corresponding build task names are: \r
- <ol>\r
- <li>min-jaba-client</li>\r
- <li>jaba-windows, jaba-complete</li>\r
- <li>jaba-without-jaxws</li>\r
- <li>jaba-no-binaries</li>\r
- <li>jaba-no-jaxws-no-binaries</li>\r
- <li>full-jaba-client</li>\r
- </ol>\r
-\r
- <p>The easiest way to build all distributives is to call <span class="hightlight">build-all </span>ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory. </p>\r
- <p class="hightlight">If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below. </p>\r
- <h4>Building web services artifacts</h4>\r
-<p>Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in <span class="hightlight">webservices/compbio/ws/server/resource</span> directory. It is not necessary to edit them if any of the JABAWS clients are used. However, if you would like to generate portable artifacts using wsimport based on the generated WSDL files then, <span class="code"><soap:address location="REPLACE_WITH_ACTUAL_URL"/></span></p>\r
-\r
-<p>must be replaced with an actual server URL including the web services context path. For example: </p>\r
-<p class="code">http://www.compbio.ac.uk:8080/ws</p>\r
-<p>JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
-</div><!-- content end--> \r
-<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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+ <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
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+ <a class="newpressed" href="index.html">Home</a> \r
+ <a class="newa" href="quick_start.html">Getting Started</a> \r
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+ <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
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<h2 id="headtitle">JABAWS 2.1</h2>\r
-<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> \r
-is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. \r
-Services for multiple sequence alignment include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
-<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
-<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. Analysis services allow\r
-prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, \r
-<a href="http://iupred.enzim.hu">IUPred</a>, Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), \r
-and <a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The \r
-secondary structure for an RNA aligment can be predicted with the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
-</p><p> \r
-<span style="color:black; font-weight:normal; text-align:left;">\r
-JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) \r
-and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r
-and sequence analysis calculations limited only by your own computing resources.<br />\r
+<p style="color:black; font-weight:normal; text-align:left;">\r
+<span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> \r
+is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently \r
+packaged to run on your local computer, server, cluster or Amazon EC2 instance.\r
+</p>\r
+\r
+<p> Services for multiple sequence alignment include \r
+<a href="http://www.clustal.org/omega">Clustal Omega</a>, \r
+<a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
+<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, \r
+<a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
+<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-Coffee</a>, \r
+<a href="http://probcons.stanford.edu/">ProbCons</a>,\r
+<a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and\r
+<a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>. \r
+Analysis services allow prediction of the protein secondary structure with \r
+<a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with \r
+<a href="http://dis.embl.de/">DisEMBL</a>, \r
+<a href="http://iupred.enzim.hu">IUPred</a>, \r
+Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and \r
+<a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation \r
+with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. \r
+The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the \r
+<a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
+</p>\r
+\r
+<p><span style="color:black; font-weight:normal; text-align:left;">\r
+JABAWS 2.1 installation can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop \r
+application</strong> (version 2.8 onwards) and the <a href="man_client.html">JABAWS command-line client</a>. \r
+JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own \r
+computing resources.<br />\r
</span></p>\r
+\r
<div id="mainpagefeatures">\r
<table>\r
<tr><td>\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 JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
+ <p>To use JABAWS web services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
</div>\r
</div>\r
<td><div class="brick">\r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
- <p><strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)</p>\r
- <p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. \r
- Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
+ <p>\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
+ to run. Please check the <a href="manual_qs_war.html#qsc">quick start guide</a> for installation instructions.\r
+ </p>\r
</div>\r
</div></td>\r
</tr>\r
</div>\r
\r
<h3 style="margin:0;">Public JABAWS Server</h3>\r
-<p> You can access our public JABA 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
+<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
<p>These web services accept submissions of less than one thousand sequences. 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://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+\r
+\r
+\r
<h3>Previous versions of JABAWS </h3>\r
-<p>We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
- contains <a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
- on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p><ul><li>\r
- <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> \r
- <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li></ul> \r
+<p>\r
+We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains \r
+<a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> \r
+for more information on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p>\r
+<ul>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> \r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>\r
+</ul> \r
+\r
+\r
+\r
<h3>Reference</h3>\r
<p><span class="hightlight">\r
</span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for \r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual</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
+<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
</head>\r
\r
<div id="page">\r
<div id="banner">\r
<table>\r
- <tr>\r
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
+ <tr>\r
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></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
</div>\r
<!-- banner end-->\r
\r
-\r
<div id="wrapper">\r
-<div id="panel"><a href="index.html">Home</a> \r
- <a 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 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="selected" href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\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://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="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a class="newpressed" href="jabaws_funding.html">Funding</a>\r
</div>\r
<!-- panel end-->\r
\r
-\r
<div id="content">\r
<h2 id="headtitle">JABAWS FUNDING</h2>\r
<p>\r
\r
<table>\r
<tr class="mid">\r
- <td class="mid"><center><a href="http://www.bbsrc.ac.uk/home/home.aspx"><img src="images/bbsrc_flat.png" width="190" height="51" alt="UK BBSRC" class="logo" title="UK BBSRC"/></a></center>\r
- <td class="mid"><center><a href="http://www.enfin.org"><img src="images/enfin.jpeg" width="210" height="60" alt="ENFIN" title="ENFIN"/></center></td>\r
- <td class="mid"><center><a href="http://www.wellcome.ac.uk"><img src="images/wellcome.jpeg" width="240" height="60" alt="Wellcome Trust" title="Wellcome Trust"/></center></td>\r
- <td class="mid"><center><a href="http://www.sulsa.ac.uk"><img src="images/sulsalogo.jpg" width="222" height="60" alt="SULSA" title="SULSA"/></center></td>\r
+ <td class="mid"><a href="http://www.bbsrc.ac.uk/home/home.aspx"><img src="images/bbsrc_flat.png" width="190" height="51" alt="UK BBSRC" class="logo" title="UK BBSRC"/></a></td>\r
+ <td class="mid"><a href="http://www.enfin.org"><img src="images/enfin.jpeg" width="210" height="60" alt="ENFIN" title="ENFIN"/></a></td>\r
+ <td class="mid"><a href="http://www.wellcome.ac.uk"><img src="images/wellcome.jpeg" width="240" height="60" alt="Wellcome Trust" title="Wellcome Trust"/></a></td>\r
+ <td class="mid"><a href="http://www.sulsa.ac.uk"><img src="images/sulsalogo.jpg" width="222" height="60" alt="SULSA" title="SULSA"/></a></td>\r
</tr>\r
</table>\r
+<br></br>\r
+<br></br>\r
</div><!-- content end-->\r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
\r
<head>\r
<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</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
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\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
</head>\r
\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
\r
<div id="wrapper">\r
-<div id="panel"><a href="index.html">Home</a> \r
- <a href="quick_start.html">Getting Started</a> \r
- <a class="selected" href="man_about.html">Manual</a> \r
- <div id="submenu">\r
- <a class="selected" href="man_about.html">About</a>\r
- <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
- <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
- <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
- <a href="man_configuration.html" >Server Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
- <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
- <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
- <a href="man_server_dev.html" >JABAWS Development</a>\r
- </div>\r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
- <a href="PublicAnnualStat" title="JABAWS 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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
+ <div id="supermenu">\r
+ <a class="newa" href="index.html">Home</a> \r
+ <a class="newa" href="quick_start.html">Getting Started</a> \r
+ <a class="newpressed" href="man_about.html">Manual</a> \r
+ </div>\r
+ <div id="submenu">\r
+ <a class="newpressed" href="man_about.html">About</a>\r
+ <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
+ <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
+ <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>\r
+ </div>\r
</div>\r
<!-- panel end-->\r
\r
<p> JABAWS currently provides access to the following programs:</p>\r
<p>Multiple Sequence Alignement </p>\r
<ul>\r
- <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
- <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
+ <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
+ <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
+ <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>\r
+ <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>\r
</ul>\r
<p>Protein Secondary structure prediction</p>\r
<ul>\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://www.compbio.dundee.ac.uk/download">Download</a> section (registration is required).\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
-<h3><a name="jaba2.1"/></a>What is new in JABAWS 2.1? </h3>\r
-<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong><p>JABAWS 2.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
+\r
+\r
+<h3><a name="jaba2.1"/>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>\r
+<p>Several new web services are available in this version of JABAWS:</p>\r
+<ul>\r
+ <li>Two multiple sequence aligners: MSAprobs and GLprobs. Both services return the standard Alignment object</li>\r
+ <li>RNAalifoldWS returns RNAStructScoreManager which is the standard ScoreManager objects with several additional methods.</li>\r
+ <li>\r
+ JpredWS returns the JpredAligment object which is the standard Alignment with additional methods for extracting \r
+ Jpred predictions. These predictions are supplied as additional sequences in the aligment.\r
+ </li>\r
+</ul>\r
+\r
+<p>Some bugs have been fixed and several improvements have been done:</p>\r
+<ul>\r
+ <li>WS status servlet returns version and some additional information on each web service</li>\r
+ <li>a bug with path to help in the client</li>\r
+ <li>Fix two bug with the Google Analytics library: no-stop due to running thread</li>\r
+ <li>GoogleAnalytics gets proper JABAWS version</li>\r
+</ul>\r
+\r
+\r
+<strong>JABAWS Version 2.0.1 (Released 2nd Jul 2013)</strong><p>JABAWS 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
<ul>\r
<li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
<li>Jronn failed to process jobs with more than 3 sequences</li>\r
- <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
+ <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
<li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores \r
in one call</li>\r
<li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\r
<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Amazon Cloud Manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</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
+<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
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+\r
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<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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- <a class="selected" href="man_about.html">Manual</a> \r
- <div id="submenu">\r
- <a href="man_about.html">About</a>\r
- <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
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- <a href="man_configuration.html" >Server Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
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- </div>\r
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- <a href="PublicAnnualStat" title="JABAWS 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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
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+ </div>\r
+ <div id="supersubmenu">\r
+ <a class="newa" href="man_about.html">About</a>\r
+ <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
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+ <div id="subsubmenu">\r
+ <a class="newa" href="man_awscloud_ec2.html" >EC2 Server</a>\r
+ <a class="newa" href="man_awscloud_bs.html" >Elastic Beanstalk</a>\r
+ </div>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
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+ <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>\r
+ </div>\r
</div>\r
<!-- panel end-->\r
\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
-<h2>JABAWS Server in the Amazon Cloud</h2>\r
-<ul>\r
- <li><a href="man_awscloud_ec2.html">How to use JABAWS on the Amazon EC2 cloud</a></li>\r
- <li><a href="man_awscloud_bs.html">How to use JABAWS WAR on Amazon Elastic Beanstalk</a> </li>\r
-</ul>\r
<div id="jabaws_on_cloud">\r
<h3><a name="jabawsOnCloud" id="jabawsOnCloud"></a>JABAWS on the Cloud</h3>\r
<p>We provide pre-configured JABAWS Amazon Machine Image (AMI) which you can use on the <a href="http://aws.amazon.com/what-is-aws">Amazon EC2 cloud</a>. Typical use cases are </p>\r
<p>If you know what to do than JABAWS AMI ID is <strong>ami-d1d5e9a5</strong>, manifest <strong>846107356395/JABAWS 2</strong> to get you started, if not please refer to <a href="man_awscloud_ec2.html">How to use JABAWS on the Amazon EC2 cloud</a> pages. </p>\r
<p>Alternatively you can use JABAWS on the <a href="http://docs.amazonwebservices.com/elasticbeanstalk/latest/dg/index.html?GettingStarted.html">Amazon Elastic BeanStalk</a>. You may want to use this option to deploy JABAWS in the cluster configuration.</p>\r
</div><!-- end of jabaws_on_cloud div -->\r
+<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>\r
</div><!-- content end-->\r
+\r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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+\r
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<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
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+\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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-<div id="panel"><a href="index.html">Home</a> \r
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- <a href="man_about.html">Manual</a> \r
- <div id="submenu">\r
- <a class="selected" href="man_about.html">About</a>\r
- <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
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- <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
- <a href="man_configuration.html" >Server Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
- <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
- <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
- <a href="man_server_dev.html" >JABAWS Development</a>\r
- </div>\r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
- <a href="PublicAnnualStat" title="JABAWS 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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
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+ <a class="newa" href="man_about.html">About</a>\r
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+ <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <div id="subsubmenu">\r
+ <a class="newa" href="man_awscloud_ec2.html" >EC2 Server</a>\r
+ <a class="newpressed" href="man_awscloud_bs.html" >Elastic Beanstalk</a>\r
+ </div>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
+ <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
+ <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>\r
+ </div>\r
</div>\r
<!-- panel end-->\r
\r
<h2>How to use JABAWS on Amazon Elastic Beanstalk</h2>\r
<div id="jabaws_on_cloud">\r
<ol>\r
- <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
- <li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console</a> and switch to AWS Elastic Beanstalk view.</li>\r
- <img src="images/aws_bs_launch.gif" alt="Elastic Beanstalk launch JABAWS war step 1" width="852" height="418">\r
- <li>Create a new Beanstalk application by uploading JABAWS war file </li>\r
- <img src="images/aws_bs_launch1.gif" alt="Elastic Beanstalk launch JABAWS war step 2" width="532" height="388"> \r
- <li>Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS. </li>\r
- <img src="images/aws_bs_launch2.gif" alt="Elastic Beanstalk launch JABAWS war step 3" width="530" height="492">\r
-\r
-<li>Choose the type of hardware you want to run JABAWS on.</li>\r
-<img src="images/aws_bs_launch3.gif" alt="Elastic Beanstalk launch JABAWS war step 4"/> \r
-<li>If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com</li>\r
-<img src="images/aws_bs_done.gif" alt="Elastic Beanstalk launch JABAWS war " width="682" height="422"> \r
+ <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>.\r
+ </li>\r
+ <li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console</a> and switch to AWS Elastic Beanstalk view.\r
+ <img src="images/aws_bs_launch.gif" alt="Elastic Beanstalk launch JABAWS war step 1" width="852" height="418" />\r
+ </li>\r
+ <li>Create a new Beanstalk application by uploading JABAWS war file:\r
+ <img src="images/aws_bs_launch1.gif" alt="Elastic Beanstalk launch JABAWS war step 2" width="532" height="388" />\r
+ </li> \r
+ <li>Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS.\r
+ <img src="images/aws_bs_launch2.gif" alt="Elastic Beanstalk launch JABAWS war step 3" width="530" height="492" />\r
+ </li>\r
+ <li>Choose the type of hardware you want to run JABAWS on.\r
+ <img src="images/aws_bs_launch3.gif" alt="Elastic Beanstalk launch JABAWS war step 4" />\r
+ </li> \r
+ <li>If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com\r
+ <img src="images/aws_bs_done.gif" alt="Elastic Beanstalk launch JABAWS war " width="682" height="422" />\r
+ </li>\r
</ol>\r
<p> </p>\r
</div><!-- end of jabaws_on_cloud div -->\r
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<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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- <div id="submenu">\r
- <a href="man_about.html">About</a>\r
- <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
- <a class="selected" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
- <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
- <a href="man_configuration.html" >Server Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
- <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
- <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
- <a href="man_server_dev.html" >JABAWS Development</a>\r
- </div>\r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
- <a href="PublicAnnualStat" title="JABAWS 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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
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+ </div>\r
+ <div id="supersubmenu">\r
+ <a class="newa" href="man_about.html">About</a>\r
+ <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <div id="subsubmenu">\r
+ <a class="newpressed" href="man_awscloud_ec2.html" >EC2 Server</a>\r
+ <a class="newa" href="man_awscloud_bs.html" >Elastic Beanstalk</a>\r
+ </div>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
+ <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
+ <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>\r
+ </div>\r
</div>\r
<!-- panel end-->\r
\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
-<h2><a name="jabawsOnCloudHow" id="jabawsOnCloudHow"/></a>How to use JABAWS on the Amazon EC2 cloud </h2>\r
+<h2><a name="jabawsOnCloudHow" id="jabawsOnCloudHow"/>How to use JABAWS on the Amazon EC2 cloud </h2>\r
<div id="jabaws_on_cloud">\r
- <ol>\r
- <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
- <li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console.</a> Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1. </li>\r
- <li>Click on "Launch Instance" button marker 2. </li>\r
-\r
-<img src="images/aws_console_launch.gif" alt="AWS console" width="687" height="704">\r
-<li>Go to the "Community AMI" tab and search for JABAWS, then click select.</li>\r
-<img src="images/aws_launch.gif" alt="select AMI" width="864" height="262">\r
- <li>Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs. If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen the hardware click continue. </li>\r
-\r
- <img src="images/aws_launch_instance.gif" alt="select hardware" width="872" height="590">\r
-\r
- <li>You should not need to customize anything on this page, continue to the next. </li>\r
-\r
- <img src="images/aws_launch_instance2.gif" alt="keys" width="872" height="592">\r
-\r
- <li> At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH. </li>\r
-\r
-<img src="images/aws_launch_instance3.gif" width="872" height="592">\r
- <li>Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance SSH is not necessary, you can do this from the Amazon Webservices Console (AWS). </li>\r
- <img src="images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588">\r
- <li>Review the configuration and launch the instance, then click "view your instances on the Instances page". </li>\r
-<img src="images/aws_launch_instance5.gif" width="870" height="430">\r
-<li>At this point you should have JABAWS instance up and running. Your AWS console should look something like this: </li>\r
-<img src="images/aws_launch_instance_done.gif" width="812" height="848">\r
-<li>Now you can consume JABAWS web services by accessing the public DNS address of your JABAWS server instance. For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public DNS address with http:// e.g. type: http://<public DNS>. The JABAWS instance on the screenshot can be accessed on http://ec2-46-137-50-196.eu-west-1.compute.amazonaws.com. </li>\r
+<ol>\r
+ <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
+ <li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console.</a> Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1. </li>\r
+ <li>Click on "Launch Instance" button marker 2.\r
+ <img src="images/aws_console_launch.gif" alt="AWS console" width="687" height="704" />\r
+ </li>\r
+ <li>Go to the "Community AMI" tab and search for JABAWS, then click select.\r
+ <img src="images/aws_launch.gif" alt="select AMI" width="864" height="262" /></li>\r
+ <li>Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs. \r
+ If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen \r
+ the hardware click continue.\r
+ <img src="images/aws_launch_instance.gif" alt="select hardware" width="872" height="590" />\r
+ </li>\r
+ <li>You should not need to customize anything on this page, continue to the next.\r
+ <img src="images/aws_launch_instance2.gif" alt="keys" width="872" height="592" />\r
+ </li>\r
+ <li> At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH. \r
+ <img src="images/aws_launch_instance3.gif" width="872" height="592" />\r
+ </li>\r
+ <li>Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if \r
+ you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance SSH is not necessary, \r
+ you can do this from the Amazon Webservices Console (AWS).\r
+ <img src="images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588" />\r
+ </li>\r
+ <li>Review the configuration and launch the instance, then click "view your instances on the Instances page".\r
+ <img src="images/aws_launch_instance5.gif" width="870" height="430" />\r
+ </li>\r
+ <li>At this point you should have JABAWS instance up and running. Your AWS console should look something like this:\r
+ <img src="images/aws_launch_instance_done.gif" width="812" height="848" />\r
+ </li>\r
+ <li>Now you can consume JABAWS web services by accessing the public DNS address of your JABAWS server instance. \r
+ For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public \r
+ DNS address with http:// e.g. type: http://<public DNS>. The JABAWS instance on the screenshot can be \r
+ accessed on http://ec2-46-137-50-196.eu-west-1.compute.amazonaws.com.\r
+ </li>\r
</ol>\r
<p>If you need to run JABAWS for large organization you might want to configure load balancer and auto scaling. Please get in contact with us if you are interested in exploring such configurations. </p>\r
<p> </p>\r
<?xml version="1.0" encoding="UTF-8"?>\r
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+\r
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<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</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
+<link href="print.css" rel="stylesheet" type="text/css" media="print" />\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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+ </div>\r
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<!-- panel end-->\r
\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h2><a name="usingcclient" id="usingcclient"></a>JABAWS Command Line Client Usage </h2>\r
-<p>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. 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 the functions which can be accessed programmatically via <a href="dm_javadoc/index.html">JABAWS API</a>. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client. </p>\r
-<span class="code"><strong>Usage:</strong> java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]<br />\r
+<p>\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
+</p>\r
+<span class="code"><strong>Usage:</strong><br/> java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]<br />\r
-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws<br />\r
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r
-</p>\r
-<br />\r
-<strong>ACTIONS:</strong><br />\r
+<br/><br/>\r
+<strong>ACTIONS:</strong><br/>\r
-i=<inputFile> - full path to fasta formatted sequence file, from which to align sequences<br />\r
-parameters - lists parameters supported by web service<br />\r
-presets - lists presets supported by web service<br />\r
-limits - lists web services limits<br />\r
Please note that if input file is specified other actions are ignored\r
-</p>\r
-<br />\r
-<strong> OPTIONS:</strong> (only for use with -i action):<br />\r
+<br/><br/>\r
+<strong> OPTIONS:</strong> (only for use with -i action):<br/>\r
-r=<presetName> - name of the preset to use<br />\r
-o=<outputFile> - full path to the file where to write an alignment<br />\r
-f=<parameterInputFile> - the name of the file with the list of parameters to use.<br />\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
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+\r
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+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\r
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+\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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+ <a class="newpressed" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
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+ </div>\r
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<!-- panel end-->\r
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<?xml version="1.0" encoding="UTF-8"?>\r
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+\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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+<?xml version="1.0" encoding="UTF-8"?>\r
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+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\r
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+\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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+ <tr>\r
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+ <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
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- <a href="man_configuration.html" >Server Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
- <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
- <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
- <a class="selected" href="man_server_dev.html" >JABAWS Development</a>\r
- </div>\r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
- <a href="PublicAnnualStat" title="JABAWS 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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
+ <div id="supermenu">\r
+ <a class="newa" href="index.html">Home</a> \r
+ <a class="newa" href="quick_start.html">Getting Started</a> \r
+ <a class="newpressed" href="man_about.html">Manual</a> \r
+ </div>\r
+ <div id="submenu">\r
+ <a class="newa" href="man_about.html">About</a>\r
+ <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
+ <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
+ <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a class="newpressed" href="man_server_dev.html" >Develop JABAWS</a>\r
+ </div>\r
</div>\r
<!-- panel end-->\r
\r
<p>Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using <span class="hightlight">build-server</span> task from <span class="hightlight">wsbuild.xml</span> ant script, than you could use build.xml tasks to generate any of the distributives you need. </p>\r
<h4><a name="projstruct" id="projstruct"></a>Structure of the project</h4>\r
<ul>\r
- <li>\r
- <span class="directory">binaries</span> contains native executables e.g. clustalw</li>\r
+ <li><span class="directory">binaries</span> contains native executables e.g. clustalw</li>\r
<ul>\r
- <li><span class="directory">src</span> contains sources of native executables</li>\r
- <li><span class="directory">windows</span> contains pre-compiled Windows binaries</li>\r
- <li>compilebin.sh - the script to complile binaries</li>\r
- <li>setexecflag.sh - the script to set executable flag for the binaries</li>\r
+ <li><span class="directory">src</span> contains sources of native executables</li>\r
+ <li><span class="directory">windows</span> contains pre-compiled Windows binaries</li>\r
+ <li>compilebin.sh - the script to complile binaries</li>\r
+ <li>setexecflag.sh - the script to set executable flag for the binaries</li>\r
</ul>\r
<li><span class="directory">conf</span> contains JABAWS configuration files </li>\r
<li><span class="directory">ExecutionStatistics</span> the database for storing collected execution statistics </li>\r
<li><span class="directory">statpages</span> the web pages for execution statistics display</li>\r
<li><span class="directory">WEB-INF</span> default </li>\r
<li><span class="directory">website</span> contains the JABAWS web pages </li>\r
- <ul>\r
- <li><span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>\r
- </ul>\r
- </ul>\r
+ <ul>\r
+ <li><span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>\r
+ </ul>\r
+</ul>\r
<h4><a name="thecode" id="thecode"></a>The code structure</h4>\r
<ul>\r
<li><span class="directory">datamodel</span> contains the JABAWS datamodel </li>\r
<p>A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.</p>\r
\r
<h4><a name="runtests" id="runtests"></a>Running tests</h4>\r
-<p>JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: <a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">Test Results</a><br/>\r
-JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a> for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases. </p>\r
+<p>\r
+JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: \r
+<a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">Test Results</a><br/>\r
+JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a> for testing. There is a TestNG plugin available for Eclipse \r
+which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied \r
+with JABAWS together with an ant tasks to run the test cases. </p>\r
<p>The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. \r
-Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster.\r
-Several testing groups are supported: \r
-<p>All tests (Test)</p>\r
-<p>Cluster tests (Run_cluster_dependent_test)</p>\r
-<p>Cluster independent tests () </p>\r
-<p>Windows only tests (All_cluster_independent_windows_only_tests) </p>\r
-<p>Performance and stability tests (Long_tests) </p>\r
-<p>Re-run failed tests (Rerun_failed_tests) </p>\r
-<p>Run custom test (CustomTest) </p>\r
+Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support \r
+of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding \r
+those that depends on the cluster.</p>\r
+<p>Several testing groups are supported:</p>\r
+<ul>\r
+<li>All tests (Test)</li>\r
+<li>Cluster tests (Run_cluster_dependent_test)</li>\r
+<li>Cluster independent tests () </li>\r
+<li>Windows only tests (All_cluster_independent_windows_only_tests) </li>\r
+<li>Performance and stability tests (Long_tests) </li>\r
+<li>Re-run failed tests (Rerun_failed_tests) </li>\r
+<li>Run custom test (CustomTest) </li>\r
+</ul>\r
<p>To run the tests you need to download all sources from <a href="#svn">repository</a>. Once you have done that, enter into the command line mode, change directory to the project directory and type: \r
<span class="code">ant -f build.xml <test group name></span> </p>\r
- <p>. Make sure you have <a href="http://ant.apache.org/">Apache Ant</a> \r
+ <p>Make sure you have <a href="http://ant.apache.org/">Apache Ant</a> \r
installed and path to ant executable is defined in your path environmental variable. \r
Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests \r
use the following \r
command: <span class="code">ant -f build.xml Run_cluster_dependent_test</span>\r
- If you work under Linux you could use a simple script from the root folder of repository called <span class="hightlight">runtests.sh</span> This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. </p>\r
- </p>\r
- <p>A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in <span class="hightlight">test-output/testng-failed.xml</span>. and is used in the ant task called <span class="hightlight">Rerun_failed_tests</span>. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: <span class="code">ant -f build.xml Rerun_failed_tests</span> CustomTest runs the test defined in the project root directory file called <span class="hightlight">temp-testng-customsuite.xml</span>. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. </p>\r
+ If you work under Linux you could use a simple script from the root folder of repository called <span class="hightlight">runtests.sh</span> \r
+ This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, \r
+ which you can define once for your system and then reuse.</p>\r
+ <p>\r
+ A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in \r
+ <span class="hightlight">test-output/testng-failed.xml</span>. and is used in the ant task called \r
+ <span class="hightlight">Rerun_failed_tests</span>. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: <span class="code">ant -f build.xml Rerun_failed_tests</span> CustomTest runs the test defined in the project root directory file called <span class="hightlight">temp-testng-customsuite.xml</span>. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. </p>\r
<p class="hightlight">For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.</p>\r
\r
<h4><a name="prepexec" id="prepexec"></a>Preparing distributive's</h4>\r
- <p>There are a number of ant tasks aimed for preparing distributives for download.\r
- Currently a few types of JABAWS packages are offered \r
- <p>Client only (contains classes required to access JABA Web Services)</p>\r
- <p>Platform specific JABAWS (windows and other)</p>\r
- <p>JABAWS without binaries</p>\r
- <p>JABAWS framework </p>\r
- </p>\r
- Corresponding build task names are: \r
- <p>min-jaba-client</p>\r
- <p>jaba-windows, jaba-complete</p>\r
- <p>jaba-no-binaries</p>\r
- <p>full-jaba-client</p>\r
- <p>The easiest way to build all distributives is to call <span class="hightlight">build-all </span>ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory. </p>\r
- <p class="hightlight">If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below. </p>\r
+ <p>There are a number of ant tasks aimed for preparing distributives for download. Currently a few types of JABAWS packages are offered:</p> \r
+ <ol>\r
+ <li>Client only (contains classes required to access JABA Web Services)</li>\r
+ <li>Platform specific JABAWS (windows and other)</li>\r
+ <li>JABAWS without binaries</li>\r
+ <li>JABAWS framework </li>\r
+ </ol>\r
+ <p>Corresponding build task names are:</p> \r
+ <ol>\r
+ <li>min-jaba-client</li>\r
+ <li>jaba-windows, jaba-complete</li>\r
+ <li>jaba-no-binaries</li>\r
+ <li>full-jaba-client</li>\r
+ </ol>\r
+ <p>The easiest way to build all distributives is to call <span class="hightlight">build-all </span>ant task. \r
+ There are more tasks defined in build.xml than described here. They are mostly self explanatory.</p>\r
+ <p class="hightlight">If you made any changes to the data model and would like to generate a complete JABAWS \r
+ distro make sure you have rebuilt jaxws artifact as described below.</p>\r
<h4><a name="buildstubs" id="buildstubs"></a>Building web services artifacts</h4>\r
-<p>Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in <span class="hightlight">webservices/compbio/ws/server/resource</span> directory. It is not necessary to edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
+<p>Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. \r
+ To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in \r
+ <span class="hightlight">webservices/compbio/ws/server/resource</span> directory. It is not necessary to \r
+ edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are \r
+ WS-I basic profile compatible. </p>\r
<h4><a name="addnewws" id="addnewws"></a>Rough guide - adding a new web service</h4>\r
<ol>\r
-<li> Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. If it has the source code and can be \r
- recompiled for different platforms include it under binaries/src.\r
- Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. </li>\r
-<li> Make sure that all the dependencies of the software being installed are satisfied. \r
- If there are other binaries they should be included as well. Keep the dependent \r
- binaries in subfolder for the main executable. Update compilebin and setexecflag </li>\r
- scripts accordingly.<li> Make sure that the new executable </li>\r
- does not have any hard links to its dependencies, e.g. is able to run from \r
- any installation folder and does not contain any hard coded paths. \r
- <li> Describe executable in conf/Exectuable.properties file. The lowercase name of the \r
- wrapper should be included in the name of the property for example Clustal \r
- properties all include clustal as a part of the name e.g. local.clustalw.bin.\r
- The same property for Mafft will be called local.mafft.bin. For more help please refer to the Executable.properties file. </li>\r
- <li> Describe the executable supported parameters in the <ExecutableName>Parameters.xml, presets in the <ExecutableName>Presets.xml and the execution limits in the <ExecutableName>Limit.xml. By convention these files are stored in conf/settings. All of these are optional. If the \r
- executable does not support parameters you do not have to mention the \r
- XXXParameter.xml file in the Executable.properties file at all. The same is true for \r
- Presets and Limits. </li>\r
-<li> Create a Java wrapper class for your executable. Create it within runner \r
- source directory. Examples of other wrappers can be found in compbio.runner.msa \r
- or compbio.runner.disorder packages. Wrapper should extend SkeletalExecutable<T> \r
- implements PipedExecutable<T> if you need to pass the input or collect the \r
- results from the standard in/out. Please see Mafft code as example. Wrapper \r
- should expend SkeletalExecutable<T> if input/output can be set as a parameter \r
- for an executable. Please see ClustalW code as example. </li>\r
-<li> Create a testcase suit for your wrapper and run the test cases. </li>\r
-<li> Create parser for the output files of your executable. Suggested location \r
- compbio.data.sequence.SequenceUtil </li>\r
-<li> Test the parser</li>\r
-<li> Decide which web services interfaces your executable is going to match. \r
- For example if the executable output can be represented as <br />\r
- SequenceAnnotation then SequenceAnnotation interface might be appropriate. \r
- For multiple sequence alignment an Msa interface should be used. </li>\r
-<li> If you find a web interface that matches your returning data type, then \r
- implement a web service which confirms to it within a webservices source folder. </li>\r
-<li> Register web service in WEB-INF/ web.xml and sun-jaxws.xml</li>\r
-<li> Add generated wsdl to wsbuild.xml ant script to generate the stubs.</li>\r
-<li> Run build-server task in wsbuild file. Watch for errors. If the task fails <br />\r
- that means that JAXB cannot serialize some of your new data structures. Add <br />\r
- appropriate annotations to your data types.\r
- Also check that <br />\r
- - you do not have interfaces to serialize. JAXB cannot serialize them.<br />\r
- - you have a default no args constructor (can be private if you do not need it)<br />\r
- - JAXB cannot serialize a Map, use custom data structure instead!<br />\r
- - Enum cannot be serialized as its abstract class (do not confuse with enum <br />\r
- which is fine)<br />\r
- - Fields serialization leave a little more space for manoeuvre, so use it. If <br />\r
- you do then you can accept and return interfaces, e.g. List, Map; abstract <br />\r
- classes etc, from your methods. <br />\r
- <br />\r
- If you have the data on the server side, but nothing is coming through to the <br />\r
- client, this is a JAXB serialization problem. They tend to be very silent and <br />\r
- thus hard to debug. Check your data structure can be serialized! </li>\r
-<li>Modify the client to work with your new web service. Update Services \r
- enumeration to include new service and ensure that all the methods of this \r
- enumeration take into account the new service. Update the client help text \r
- (client_help.txt) and insert it into the Constraints class. </li>\r
-<li> Test the web service with the client </li>\r
-<li> Test on the cluster.</li>\r
+ <li> \r
+ <p>Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. \r
+ If it has the source code and can be recompiled for different platforms include it under \r
+ <span class="hightlight">binaries/src</span>. Edit <span class="hightlight">setexecutableflag.sh</span> \r
+ and <span class="hightlight">compilebin.sh</span> scripts in <span class="hightlight">binaries/src</span> \r
+ accordingly.</p>\r
+ </li><li>\r
+ <p>Make sure that all the dependencies of the software being installed are satisfied. \r
+ If there are other binaries they should be included as well. Keep the dependent \r
+ binaries in a subfolder for the main executable. Update \r
+ <span class="hightlight">compilebin.sh</span> and <span class="hightlight">setexecflag.sh</span> scripts accordingly.</p>\r
+ </li><li>\r
+ <p>Make sure that the new executable does not have any hard links to its dependencies, e.g. is able to run from \r
+ any installation folder and does not contain any hard coded paths.</p>\r
+ </li><li>\r
+ <p>Describe executable in <span class="hightlight">conf/Exectuable.properties</span> file. The lowercase name of the wrapper should be included \r
+ in the name of the property for example Clustal properties all include clustal as a part of the name e.g. local.clustalw.bin.\r
+ The same property for MAFFT will be called local.mafft.bin. For more help please refer to the Executable.properties file.</p>\r
+ </li><li>\r
+ <p>Describe the executable supported parameters in the \r
+ <span class="hightlight"><ExecutableName>Parameters.xml</span>, presets in the \r
+ <span class="hightlight"><ExecutableName>Presets.xml</span> and the execution limits in the \r
+ <span class="hightlight"><ExecutableName>Limit.xml</span>. By convention these files are stored \r
+ in <span class="hightlight">conf/settings</span>. All of these are optional. If the executable \r
+ does not support parameters you do not have to mention the <span class="hightlight">XXXParameter.xml</span> file \r
+ in the <span class="hightlight">Executable.properties</span> file at all. The same is true for \r
+ Presets and Limits.</p>\r
+ </li><li>\r
+ <p>Create a Java wrapper class for your executable. Create it within <span class="hightlight">runner</span> source directory. \r
+ Examples of other wrappers can be found in <span class="hightlight">compbio.runner.msa</span> or \r
+ in other <span class="hightlight">compbio.runner.*</span> packages. Wrapper should extend \r
+ <span class="hightlight">SkeletalExecutable<T></span> and implement \r
+ <span class="hightlight">PipedExecutable<T></span> \r
+ if you need to pass the input or collect the results from the standard in/out. Please see Mafft \r
+ code as example. Wrapper should expend <span class="hightlight">SkeletalExecutable<T></span> \r
+ if input/output can be set as a parameter for an executable. Please see the ClustalW code as example.</p>\r
+ </li><li>\r
+ <p>Create a testcase suit for your wrapper in <span class="hightlight">testsrc</span> and run the test cases.</p>\r
+ </li><li>\r
+ <p>Create parser for the output files of your executable. Suggested location \r
+ compbio.data.sequence.SequenceUtil </p>\r
+ </li><li>\r
+ <p>Test the parser</p>\r
+ </li><li>\r
+ <p>Decide which web services interfaces your executable is going to match. For example \r
+ if the executable output can be represented as SequenceAnnotation then SequenceAnnotation \r
+ interface might be appropriate. For multiple sequence alignment an Msa interface should be used.</p>\r
+ </li><li>\r
+ <p>If you find a web interface that matches your returning data type, then \r
+ implement a web service which confirms to it within a webservices source folder. </p>\r
+ </li><li> \r
+ <p>Register web service in <span class="hightlight">WEB-INF/web.xml</span> \r
+ and <span class="hightlight">WEB-INF/sun-jaxws.xml</span></p>\r
+ </li><li> \r
+ <p>Add generated wsdl to wsbuild.xml ant script to generate the stubs.</p>\r
+ </li><li>\r
+ <p>Run build-server task in wsbuild file. Watch for errors. If the task fails that means \r
+ that JAXB cannot serialize some of your new data structures. Add appropriate annotations to your data types.\r
+ Also check that: </p>\r
+ <ul>\r
+ <li>you do not have interfaces to serialize, since JAXB cannot serialize them;</li>\r
+ <li>you have a default no args constructor (can be private if you do not need it);</li>\r
+ <li>JAXB cannot serialize Java Map class, use a custom data structure instead;</li>\r
+ <li>Enum cannot be serialized as its abstract class (do not confuse with enum which is fine);</li>\r
+ <li> Fields serialization leaves a little more space for manoeuvre. \r
+ If you do this then you may accept<br/> and return interfaces, e.g. List, Map; abstract classes etc, from your methods.\r
+ </li>\r
+ </ul>\r
+ <p>If you have the data on the server side, but nothing is coming through to the \r
+ client, this is a JAXB serialization problem. They tend to be very silent and \r
+ thus hard to debug. Check your data structure can be serialized!</p>\r
+ </li><li>\r
+ <p>Modify the client to work with your new web service. Update Services \r
+ enumeration to include new service and ensure that all the methods of this \r
+ enumeration take into account the new service. Update the client help text \r
+ (client_help.txt) and insert it into the Constraints class.</p>\r
+ </li><li>\r
+ <p>Test the web service with the client.</p>\r
+ </li><li> \r
+ <p>Test on the cluster.</p>\r
+ </li>\r
</ol>\r
<p> </p>\r
</div><!-- content end-->\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
\r
-\r
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+\r
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<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\r
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<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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<!-- panel end-->\r
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-\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and \r
VMware Fusion on Mac. \r
However, you are not limited to these virtualization systems and can use the JABAWS appliance with any other virtualization platform. You can use <a href="http://communities.vmware.com/community/vmtn/server/vsphere/automationtools/ovf">VMware OVF tool</a> to prepare JABAWS image for a different virtualization platform e.g. <a href="http://www.virtualbox.org/">VirtualBox</a>.</p>\r
-<h3><a name="whenvm" id="whenvm"/></a>When to use the JABAWS Virtual Appliance</h3>\r
+<h3><a name="whenvm" id="whenvm"/>When to use the JABAWS Virtual Appliance</h3>\r
<p>The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access \r
systems over an internet, or just want to keep their data private. It is also \r
the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run.</p>\r
<em>Access:</em> root@VM_IP</li>\r
</ul>\r
<p>Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. </p>\r
-<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h3>\r
-<p>After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
+\r
+\r
+<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</h3>\r
+<p>\r
+After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. \r
+To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> \r
+New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview \r
+<a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.\r
+</p>\r
<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>\r
<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>\r
<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>\r
<p>If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.</p>\r
-<h3><a name="vmiaccess" id="vmiaccess"/></a></a>VM Network Settings </h3>\r
-<p>By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)</a></p>\r
+<h3><a name="vmiaccess" id="vmiaccess"/>VM Network Settings </h3>\r
+<p>\r
+By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, \r
+but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect \r
+to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host \r
+in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use \r
+a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP \r
+server to do that)</p>\r
</div><!-- content end-->\r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
<?xml version="1.0" encoding="UTF-8"?>\r
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+\r
<head>\r
<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</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
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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+<div id="panel">\r
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+ </div>\r
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<!-- panel end-->\r
\r
-\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<p><span class="code">Connecting to service ProbconsWS on http://localhost:8080/ws ... OK<br />\r
Testing alignment with default parameters:FAILED<br />\r
Service ProbconsWS IS NOT FUNCTIONAL</span>If the web server did not respond the message looks like following: <span class="code">Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED</span></p>\r
-<h3><a name="diffcontexts" id="diffcontexts"/></a></a>Running many JABAWS instances on the same server</h3>\r
+<h3><a name="diffcontexts" id="diffcontexts"/>Running many JABAWS instances on the same server</h3>\r
<p> JABAWS is supplied as a Web Application aRchive which can be dealt with as any other web applications. So it is perfectly possible to run two JABAWS instances from the same server. Just make two different contexts on your application server and unpack JABAWS in both of them. For example if your server name is http://www.align.ac.uk, and the context names are public and private. Than one group of users could be given a URL http://www.align.ac.uk/public and another http://www.align.ac.uk/private. These contexts will be served by two independent JABAWS instances, and could be configured differently. If you keep local engine enabled, make sure you reduce the number of threads local engine is allowed to use to avoid overloading the server. Alternatively two completely separate web application server instances (e.g. Apache-Tomcat) could be used. This will give you a better resilience and more flexibility in memory settings. </p>\r
<h3><a name="nocluster" id="nocluster"></a>JABAWS on a single server</h3>\r
<p>You can run JABAWS on a single server. Obviously the capacity will be limited, but may be sufficient for a small lab. Installed on a single server, JABAWS executes tasks in parallel, so the more cores the server has the more requests it will be able to handle. </p>\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\r
<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</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
+<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
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+\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
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- </div>\r
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- <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 href="jabaws_funding.html">Funding</a>\r
+<div id="panel">\r
+ <div id="supermenu">\r
+ <a class="newa" href="index.html">Home</a> \r
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+ </div>\r
+ <div id="submenu">\r
+ <a class="newa" href="man_about.html">About</a>\r
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+ <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a class="newa" href="man_configuration.html" >Configure JABAWS</a>\r
+ <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>\r
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+ </div>\r
</div>\r
<!-- panel end-->\r
\r
-\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<p>JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. Each month is a link to the detailed usage statistics for this month described later. Please note however, that the links to the detailed monthly statistics are only available for authenticated users in the role <span class="hightlight">admin</span>. There is a link at the bottom of the page that would let you login, if you have not done so. </p>\r
<p>If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, e.g. empty. </p>\r
<p>If you have deployed a JABAWS WAR file, then please see the <a href="#conf_tomcat_user">configuring privileged access for Tomcat web application server</a> section for further details. </p>\r
-<p><img src="images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318"></p>\r
+<p><img src="images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318" /></p>\r
<p>The table contains the number of jobs processed by JABAWS per month, for the whole period when the statistics was collected</p>\r
<p>For each month the table contains the following information.</p>\r
<ul>\r
<p>Authentication lets you see the detailed usage statistics. If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, e.g. empty. In other cases you need to ask your system administrator for it. </p>\r
<h3><a name="detailed_usage"></a>Detailed Usage Statistic </h3>\r
<p>Detailed execution statistics for each month is available for authenticated users only. </p>\r
-<p><img src="images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902"></p>\r
+<p><img src="images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902" /></p>\r
<p>Each table contains the number of jobs processed by JABAWS during the period of time specified in the title.</p>\r
<ul>\r
<li>The "All Jobs" table contains the summary of all jobs.</li>\r
</ul>\r
<h3><a name="job_list"></a>Job List </h3>\r
<p>Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view the application server may need to be configured. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
-<p><img src="images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198"> </p>\r
+<p><img src="images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>\r
<p>Columns </p>\r
<ul>\r
<li>JobID - the JABAWS job id, unique for every job</li>\r
<li>isFinished - whether the job has finished. This does not necessarily mean that the job has produced the result. The job can sometime finish in failure.</li>\r
</ul>\r
<h3><a name="job_dir"></a>JABAWS Job Directory Content </h3>\r
-<p><img src="images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420"></p>\r
+<p><img src="images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420" /></p>\r
<p>STARTED and FINISHED files contain Unix timestamp - when the job was started and completed respectively. STARTED is replaced by SUBMITTED if the job has been submitted to the cluster, as opposed to executed locally, on the server. </p>\r
<p>COLLECTED file is empty and indicates that the job results were collected by the user. Due to asynchronous nature of the job it is possible that the job was started and finished, but the results has never been requested. </p>\r
<p>RunnerConfig.xml file contains a complete description of the job and JABAWS can restart the job based on this description. </p>\r
<h3><a name="exec_stat_conf"></a>Configuring JABAWS execution statistics</h3>\r
<p>JABAWS execution statistics is a multi-component system. First is a crawler which job is to collect and preprocess the statistics from the job temporary directories and record the collected statistics into the database. The second part of the system is a web application which job is to visualise the statistics from the database. </p>\r
<p>It is possible to enable/disable the statistics collector by changing the following properties in the conf/Cluster.engine.properties and conf/Local.engine.properties files. </p>\r
-<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br>\r
+<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br/>\r
cluster.stat.collector.enable=false\r
<br/>\r
- # Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h) <br>\r
+ # Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h) <br/>\r
cluster.stat.maxruntime=24</p>\r
-<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br>\r
+<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br/>\r
local.stat.collector.enable=true\r
<br/>\r
- # Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours<br>\r
+ # Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours<br/>\r
local.stat.maxruntime=6</p>\r
<p>If the statistics collector is enabled then the crawler starts automatically soon after (10 minutes for local engine, and 60 minutes for cluster engine) the JABAWS web application and will be collecting the execution statistics every 24 hours after the start. </p>\r
<p>The details of the job are only available if the job temporary directory is located within a JABAWS web application. If not, the system administrator can create a symbolic link pointing to the temporary job directories outside of a web application and configure the application server to allow navigation to the links. For the Tomcat application server the context configuration file should be created and copied to the <TOMCAT_ROOT>/conf/Catalina/localhost directory. The name of the file should be the same as the web application context name, for example "<span class="hightlight">jabaws.xml</span>" for jabaws. Where the TOMCAT_ROOT is the location of the Tomcat web application server. Here is an example of such a file: </p>\r
-<p><span class="code"><?xml version="1.0" encoding="UTF-8"?><br>\r
+<p><span class="code"><?xml version="1.0" encoding="UTF-8"?><br/>\r
<Context antiResourceLocking="false" privileged="true" allowLinking="true"/></span></p>\r
<p>The key option here is this: <span class="hightlight">allowLinking="true"</span>. Please also make sure that you have defined the user in role "<span class="hightlight">admin</span>" as described <a href="#conf_tomcat_user">below</a>.</p>\r
<h3><a name="conf_tomcat_user" id="conf_tomcat_user"></a>Configuring a privileged access for Tomcat web application server</h3>\r
<user username="peter" password="your password here " roles="admin"/><br/>\r
</tomcat-users></span></p>\r
<p>For more information on users and roles please consult Apache-Tomcat help pages. </p>\r
-<p><br>\r
+<p><br/>\r
</p>\r
</div><!-- content end-->\r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
<?xml version="1.0" encoding="UTF-8"?>\r
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<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\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
+<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
</head>\r
\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\r
<table>\r
- <tr>\r
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
+<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" 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
-</div>\r
-<!-- banner end-->\r
-\r
+</div><!-- banner end-->\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></div>\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://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="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
\r
\r
<li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
<li>Configure JABAWS either on the <a href="man_awscloud_ec2.html">Amazon EC2 cloud</a> or on <a href="man_awscloud_bs.html">Amazon Elastic Beanstalk</a></li>\r
</ol>\r
-</div><!-- about end-->\r
</div><!-- content end--> \r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\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
+<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
</head>\r
\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\r
<table>\r
- <tr>\r
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
+<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" 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
-</div>\r
-<!-- banner end-->\r
+</div><!-- banner end-->\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></div>\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://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="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
\r
+\r
<div id="content">\r
<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
</tr>\r
</table>\r
\r
-\r
<a name="qsc"/>\r
<h3><a name="client"/>The JABAWS command line client</h3>\r
<ul><li><a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar</a> (80 K)</li>\r
<ul>\r
<li><span class="hightlight">java -jar jaba-client.jar</span></li>\r
</ul>\r
-\r
+</p>\r
<p>\r
A JABA Web Services are WS-I compliant. This means that you can access them from any \r
language that has libraries or functions for consuming interoperable SOAP web services.\r
<!-- TODO Provide list of libraries for different languages -->\r
</p>\r
-</div><!-- about end-->\r
</div><!-- content end--> \r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\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
+<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
</head>\r
\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\r
<table>\r
- <tr>\r
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
+<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" 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
-</div>\r
-<!-- banner end-->\r
+</div><!-- banner end-->\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></div>\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://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="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
\r
-\r
<div id="content">\r
<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
</tr>\r
</table>\r
\r
-\r
<a name="qsc"/>\r
<h3>Running JABAWS on your local machine</h3>\r
<ul><li>Download <a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance</a> (520M) </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
- virtual machine on your laptop or desktop computer. A <a href="man_servervm.html#whenvm">complete guide \r
- to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:\r
-\r
+The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a \r
+virtual machine on your laptop or desktop computer. A <a href="man_servervm.html#whenvm">complete guide \r
+to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:\r
+</p>\r
<p>If you work on Windows, Linux or Unix </p>\r
<ol>\r
<li>download and install <a href="http://www.vmware.com/products/player">VMWare Player</a>.</li>\r
<li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>\r
</ol>\r
</div>\r
-</div><!-- about end-->\r
</div><!-- content end--> \r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\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
+<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
</head>\r
\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\r
<table>\r
- <tr>\r
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" 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
+<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" 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
-</div>\r
-<!-- banner end-->\r
+</div><!-- banner end-->\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></div>\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://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="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
\r
+\r
<div id="content">\r
<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\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://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 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
\r
#panel a:link, a:visited {\r
- text-decoration: none;\r
+ text-decoration: none;\r
display:block;\r
line-height: 1em;\r
padding:10px;\r
color:#000000; \r
text-decoration:none;\r
- }\r
- \r
+ }\r
+\r
#panel a:hover {\r
- background-color: transparent;\r
- text-decoration: underline;\r
+ background-color: transparent;\r
+ text-decoration: underline;\r
}\r
\r
\r
}\r
\r
.hightlight { \r
-font-style:italic;\r
-font-family:"Courier New", Courier, monospace;\r
+ font-style:italic;\r
+ font-family:"Courier New", Courier, monospace;\r
}\r
\r
.code { \r
<?xml version="1.0" encoding="UTF-8"?>\r
-<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\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
+<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
</head>\r
\r
<body>\r
<div id="page">\r
+\r
<div id="banner">\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/jabaws25.png" width="263" height="60" 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 href="jabaws_funding.html">Funding</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://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="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
\r
-\r
<div id="content">\r
<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
.brick {\r
padding-bottom:1em;\r
border: 2px solid #999;\r
- -webkit-border-radius:20px;\r
- -moz-border-radius:20px;\r
+ -webkit-border-radius:10px;\r
+ -moz-border-radius:10px;\r
border-radius: 20px;\r
background-image:url(images/brickhead2_line.jpg);\r
background-repeat:repeat-x;\r
padding: 2em 1.5em 0em 1.5em;\r
}\r
\r
-#panel {\r
- width:161px;\r
- background:url("images/panel_bg_long.png") repeat-y ;\r
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- font-family:Verdana, Arial, Helvetica, sans-serif;\r
- padding-top:1em;\r
-}\r
-\r
#content {\r
margin-left:170px;\r
border-bottom:solid 1px #6994af;\r
list-style-type: circle;\r
}\r
\r
-#panel a:link, #panel a:visited {\r
- text-decoration: none;\r
- display:block;\r
- line-height: 1em;\r
- padding:10px;\r
- color:#000000;\r
-}\r
-\r
-#panel a:hover {\r
- background-color: transparent;\r
- text-decoration: underline;\r
-}\r
\r
-#panel a.selected {\r
- text-decoration:underline;\r
- font-weight:bolder;\r
-}\r
-\r
-#panel #submenu a {\r
- margin-left: 1.5em;\r
- margin-left: 20px;\r
- padding: 5px;\r
-}\r
\r
strong {\r
font-weight:bold;\r
display:block;\r
}\r
\r
+.mid {\r
+ vertical-align:middle;\r
+ height:80px;\r
+ border:none;\r
+}\r
+\r
.u {\r
text-decoration: underline;\r
}\r
float:left;\r
}\r
\r
-.mid {\r
- vertical-align:middle;\r
- height:80px;\r
- border:none;\r
+/***************************************************************************************/\r
+/************************************ panel styles *************************************/\r
+#panel {\r
+ width:160px;\r
+/* margin-left: -150px;*/\r
+ background:url("images/panel_bg_long.png") repeat-y ;\r
+ float:left;\r
+ font-family:Verdana, Arial, Helvetica, sans-serif;\r
+ padding-top:1em;\r
+}\r
+\r
+#panel a:link, #panel a:visited {\r
+ line-height: 1em;\r
+ font-size: 12pt;\r
+ margin: 15px auto;\r
+ width: 95px;\r
+ text-align: center;\r
+}\r
+\r
+#panel #supermenu a {\r
+ margin-left: 10px;\r
+}\r
+\r
+#panel #submenu a {\r
+ margin-left: 30px;\r
}\r
\r
+#panel #supersubmenu a {\r
+ margin-left: 25px;\r
+}\r
+\r
+#panel #subsubmenu a {\r
+ margin-left: 40px;\r
+}\r
+\r
+#panel a.newa {\r
+ color: #888888;\r
+ text-decoration: none;\r
+ background-color: rgba(219,87,5,1);\r
+ background-image:url("images/banner_bg.gif");\r
+ font-family: 'Yanone Kaffeesatz';\r
+ font-weight: 400;\r
+ display: block;\r
+ padding: 4px;\r
+ -webkit-border-radius: 6px;\r
+ -moz-border-radius: 6px;\r
+ border-radius: 6px;\r
+ -webkit-box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+ -moz-box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+ box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+}\r
+\r
+#panel a.newpressed {\r
+ color: #FFFFFF;\r
+ text-decoration: none;\r
+ background-image:url("images/banner_bg.gif");\r
+ background-color: #F5F5F5;\r
+ font-family: 'Yanone Kaffeesatz';\r
+ font-weight: 700;\r
+ display: block;\r
+ padding: 4px;\r
+ -webkit-border-radius: 8px;\r
+ -moz-border-radius: 8px;\r
+ border-radius: 8px;\r
+ -webkit-box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+ -moz-box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+ box-shadow: 0px 9px 0px #888888, 0px 9px 25px rgba(0,0,0,.7);\r
+}\r
+\r
+#panel a:active {\r
+ -webkit-box-shadow: 0px 3px 0px rgba(219,31,5,1), 0px 3px 6px rgba(0,0,0,.9);\r
+ -moz-box-shadow: 0px 3px 0px rgba(219,31,5,1), 0px 3px 6px rgba(0,0,0,.9);\r
+ box-shadow: 0px 3px 0px rgba(219,31,5,1), 0px 3px 6px rgba(0,0,0,.9);\r
+ position: relative;\r
+ top: 6px;\r
+}\r
git://source.jalview.org / jabaws.git / commitdiff