<!--body end -->\r
</div>\r
\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
\r
\r
<!-- panel end-->\r
<div id="content">\r
- <h2 id="headtitle" style="text-align:left">JABAWS Server Virtual Machine</h2>\r
- <p><span style="text-align:left">JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend <a href="http://www.vmware.com/products/player">VMWare Player</a> for Windows and Linux users or <a href="http://www.vmware.com/products/fusion/overview.html">VMware Fusion</a> for Mac users. <a href="http://www.jalview.org/download.html">Jalview</a></span> can <a href="man_servervm.html#jalviewWithJaba">use your local JABAWS VM</a>. </p>\r
+ <h2 id="headtitle" style="text-align:left">JABAWS Server Virtual Appliance </h2>\r
+ <p><span style="text-align:left">JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend <a href="http://www.vmware.com/products/player">VMWare Player</a> for Windows and Linux users or <a href="http://www.vmware.com/products/fusion/overview.html">VMware Fusion</a> for Mac users. <a href="http://www.jalview.org/download.html">Jalview</a></span> can <a href="man_servervm.html#jalviewWithJaba">use your local JABAWS VA</a>. </p>\r
<ul>\r
- <li> JABAWS Virtual Appliance: <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip">download</a> (520M)</li>\r
+ <li> JABAWS Virtual Appliance: <a href="archive/jabaws-vm.zip">download</a> (520M)</li>\r
</ul>\r
<p>Please check out our <a href="man_servervm.html#whenvm">manual</a> for the detailed instructions. </p>\r
\r
<!-- Note - mention servlet 2.4 compliance here? -->\r
supporting at the Java servlet specification v. 2.4 or above, i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 7.0</a>. </p>\r
<ul>\r
-<li>A Complete Server for all platforms: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">download</a>\r
-(51M)</li>\r
+<li>A JABAWS WAR for all platforms (comes with precompiled Linux x86 and Windows binaries): <a href=\r
+"archive/jaba.war">download</a>\r
+(55M)</li>\r
+<li>A JABAWS WAR for Mac (comes with precompiled Mac binaries): <a href=\r
+"archive/jabaws.war">download</a> (51M)</li>\r
</ul>\r
\r
\r
-<p>Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VM package instead. \r
+<p>Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VA package instead. \r
<!-- content end-->\r
</p>\r
\r
<li>Command line client\r
<ul>\r
<li>binaries: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">download</a> (80 K)</li>\r
+"archive/min-jaba-client-2.0.jar">download</a> (80 K)</li>\r
<li>source: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">download</a> (70 K)</li>\r
+"archive/jaba-client-src-2.0.jar">download</a> (70 K)</li>\r
</ul>\r
</li>\r
</ul>\r
<p>The command line client will display help documentation if it is run with no arguments, the same information is also given in <a href="man_client.html#usingcclient">the command line client's manual page</a>. </p>\r
<h2>Version </h2>\r
-<p>Current JABAWS version is 1.1 release date 7 April 2011. Please consult the <a href="change.log">change log</a> file for the breakdown of the changes. </p>\r
+<p>Current JABAWS version is 2.0 release date 15 August 2011. </p>\r
<div class="source">\r
<div class="header collapsed" onclick=\r
"$(this).toggleClassName('collapsed'); $(this).next('.body').toggleClassName('collapsed');"\r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
<p><strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M) </p>\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (55M) </p>\r
<p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
</div>\r
</div></td>\r
<div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
<div class="brick_content">\r
<strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M)\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (55M)\r
<br/>\r
<strong>The Client: </strong>\r
Command Line Client <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">binary</a> | <a href=\r
title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
"nofollow">WSDL List</a></li>\r
</ul>\r
-<p>The maximum number of sequences you can align with this public web service is 1000 with up to 1000 letters average length. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can <a href="quick_start.html">download</a> and run the JABAWS Server on your own hardware.</p>\r
+<p>These web services will reject submissions containing more then one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can <a href="quick_start.html">download</a> and run the JABAWS Server on your own hardware.</p>\r
\r
\r
-<h3>Publication</h3>\r
+<h3>Reference</h3>\r
<p><span class="hightlight"></span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" <span class="i">Bioinformatics</span> 2011; <a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&ijkey=gd0DwuYBzFRhe4T">doi: 10.1093/bioinformatics/btr304</a>.</p>\r
</div>\r
\r
<p>JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need. </p>\r
<h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\r
<ul>\r
-<li>Can be deployed on most operating systems, as a VMWare or OpenBox compatible Virtual Appliance or a Tomcat Java Web Application.</li>\r
+<li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>\r
<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>\r
<li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>\r
<li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>\r
</div> \r
<!-- about end-->\r
<!-- content end--> \r
-<div id="copyright">Last update: 1 April 2011<br/>\r
+<div id="copyright">Last update: 10 August 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
\r
</div>\r
</div>\r
\r
<!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
</table>\r
</div>\r
<!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
<ul>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/DisEMBLWS?wsdl">DisEMBLWS</a> (http://www.compbio.dundee.ac.uk/jabaws/DisEMBLWS?wsdl) </li>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl) </li>\r
</ul>\r
<p>Amino acid conservation service</p>\r
<ul>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl">AAConWS</a> (http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl) </li>\r
-</ul>\r
+ </ul>\r
+<p>Please replace <span class="hightlight">http://www.compbio.dundee.ac.uk/</span> with your JABAWS instance host name, and <span class="hightlight">jabaws</span> with your JABAWS context name to access your local version of JABAWS web services. For example <span class="hightlight">http://localhost:8080/jabaws</span> would be a valid URL for the default Apache-Tomcat installation and jabaws.war file deployment. </p>\r
<h3><a name="defalign" id="defalign"></a>Aligning sequences </h3>\r
<p>Given that <span class="hightlight">msaws</span> is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows: </p>\r
<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
</div>\r
\r
<!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
Web Application Archive (WAR) on TurnKey Linux. Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it.<br/>\r
You can run the appliance with freely available program such as <a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it first. We have tested the JABAWS appliance \r
with VMware Player v 3.1.2 on Windows and Linux, and 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 convert JABAWS image to a different virtualization format e.g. OVF.</p>\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
<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
version 2.4 of the Java Servlet specification, and a Java 6 runtime\r
environment. We recommend using an official Oracle Java 6 runtime\r
environment, and <a\r
-href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> web application server version 6, but other versions may work as well.<br/><span class="attention">Please Note:</span> The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.</p>\r
+href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a> web application server version 7, but older Tomcat versions above 5.5 would work too.<br/>\r
+<span class="attention">Please Note:</span> The JABAWS WAR is not generally compatible with older Mac systems based on the PowerPC architecture, since Java 1.6 is not available to run JABAWS.</p>\r
\r
-<p>JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform.\r
+<p>JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, not all web services are currently available for MS Windows platform.\r
<!-- todo: link to help about obtaining and installing tomcat -->\r
</p>\r
-<p>JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries, as well as the source code and build scripts necessary to recompile them.</p>\r
+<p>JABAWS comes with pre-compiled MS Windows and Linux x86 binaries, as well as the source code and build scripts necessary to recompile them.</p>\r
<p>To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes. </p>\r
<h3><a name="instwar" id="instwar"></a>Installing the JABAWS WAR file</h3>\r
<p>JABAWS is distributed as a web application archive (WAR). To\r
<h2><a name="usingcclient" id="usingcclient"></a>JABAWS Usage Statistics </h2>\r
<ul>\r
<li><a href="#usage_sum">Summary of Usage</a></li>\r
+ <li><a href="#helpUsageStats">Authentication</a></li>\r
<li><a href="#detailed_usage">Detailed Usage Statistic </a></li>\r
<li><a href="#job_list">Job List</a></li>\r
<li><a href="#job_dir">Single Job Directory Content </a></li>\r
<li>Abandoned - the number of jobs which result(s) were not collected</li>\r
</ul>\r
<p>The summary for each column is displayed in the last row of the table.</p>\r
+<h3><a name="helpUsageStats"></a>Authentication</h3>\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
</div>\r
\r
<!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
<ul><li><a href=\r
"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">Download the Client Jar</a> (80 K)</li>\r
</ul>\r
-</p>\r
<p>This is a single java archive which contains the JABAWS command line client. \r
It requires Java version 1.6 to run, and allows anyone who wants to connect \r
to and to use JABAWS from their own software. \r
You can read more about how to use command line client <a href="man_client.html">in the CMD Client</a> section of the manual. \r
You can also get command line help by changing to the directory where you downloaded the client jar, and typing:\r
<ul>\r
- <li><span class="hightlight">java -jar min-jaba-client.jar</span></li>\r
-</ul></p>\r
+ <li><span class="hightlight">java -jar jaba-client.jar</span></li>\r
+</ul>\r
<p>A JABAWS server's 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
<!-- PETER TODO Provide list of libraries for different languages --></p>\r
<!-- about end-->\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 1 April 2011<br/>\r
+<div id="copyright">Last update: 10 August 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
<li>download and install <a href="http://www.vmware.com/products/player">VMWare Player</a>.</li>\r
<li>Unpack the JABAWS virtual appliance and open it with VMware Player.</li>\r
</ol>\r
+<p>If you work on Mac do the same using <a href="http://www.vmware.com/products/fusion/overview.html">VMware Fusion</a>, or for free alternative use a WAR JABAWS package. </p>\r
<div id="testing_jabaws">\r
<h3>Testing</h3>\r
<p>The easiest way to test that your JABAWS Virtual appliance is working is to use Jalview.</p>\r
<!-- about end-->\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 1 April 2011<br/>\r
+<div id="copyright">Last update: 1 August 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
<p>This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.</p>\r
\r
<ol>\r
-<li>Download the <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS WAR with all binaries</a> (45M)</li>\r
- <li>Download and install <a href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a>.<br/>\r
- <span class="hightlight">You will need at least version 5.5 of Tomcat (we would recommend version 6.0) and at least version 1.6 (i.e. JAVA 6) of Java.</span></li>\r
+<li>Download the <a href="http://www.compbio.dundee.ac.uk/jabaws/download.html">JABAWS WAR for your platform </a></li>\r
+ <li>Download and install <a href="http://tomcat.apache.org/download-70.cgi">Apache-Tomcat</a>.<br/>\r
+ <span class="hightlight">You will need at least version 5.5 of Tomcat (we would recommend version 7.0) and at least version 1.6 (i.e. JAVA 6) of Java.</span></li>\r
<li>Drop the JABAWS WAR file into <span class="hightlight">tomcat/webapps</span> directory.</li>\r
<li>(Re)start the Tomcat.</li>\r
<li>Once the tomcat has started, it should automatically unpack the WAR into the webapps directory (if it doesn't, then you'll need to do this manually, it's just a zip archive in the end).</li>\r
<li>You then need to complete the installation of the executable binaries:</li>\r
- <ul><li>If you are on Linux<br/><span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./setexecflag.sh </span> script to ensure the JABAWS binaries can be executed. </li>\r
- <li>If you are on a Mac (OSX intel mac only) or other unix-like architecture with gnu compilers available:</li>\r
+ <ul>\r
+ <li>If you are on Linux or Mac (OSX intel Mac only) <br/>\r
+ <span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./setexecflag.sh </span> script to ensure the JABAWS binaries can be executed. </li>\r
+ <li>If you are on other unix-like architecture with gnu compilers available or you'd like to get a maximum performance:</li>\r
<li> <span class="hightlight">cd</span> to <span class="hightlight">webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./compilebin.sh </span> script to compile all binaries JABAWS depends on. </li>\r
<li><span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/ </span>and execute <span class="hightlight">./setexecflag.sh </span> script. </li>\r
</ul>\r
<p>You can test that your JABAWS server is working in two ways.</p>\r
<ol>\r
<li>If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running:\r
-<span class="code">java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h http://localhost:8080/jabaws</span>\r
+<span class="code">java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws</span>\r
In this example we assumed that your JABAWS server URL is <span class="hightlight">http://localhost:8080</span> and JABAWS context path is <span class="hightlight">jabaws</span>\r
</li>\r
\r
<!-- TODO put JABAWS CMD test instructions here -->\r
</div> <!-- content end-->\r
<!-- about end-->\r
-<div id="copyright">Last update: 1 April 2011<br/>\r
+<div id="copyright">Last update: 10 August 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
\r
</div><!-- wrapper end -->\r
<!-- about end-->\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 1 April 2011<br/>\r
+<div id="copyright">Last update: 10 August 2011<br/>\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
git://source.jalview.org / jabaws.git / commitdiff