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<div id="content">\r
-<h2>JABAWS Manual</h2>\r
-\r
-<h4>JABAWS Installation</h4>\r
-\r
-<h5>System Requirements</h5>\r
-\r
-<p>JABAWS requires a java web application server compliant with\r
-version 2.4 of the java servlet specification, and a java 6 runtime\r
-environment. We recommend using an official Sun Java 6 runtime\r
-environment, but others may work. We have tested JABAWS with <a\r
-href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat\r
-version 6</a>, however we expect it will also be compatible with <a\r
-href="http://tomcat.apache.org/download-55.cgi">version\r
-5.5</a>.</p>\r
-\r
-<!-- todo: link to help about obtaining and installing tomcat -->\r
-<h5>Installing the JABAWS WAR file</h5>\r
-\r
-<p>JABAWS is distributed as a web application archive (WAR). To\r
-deploy JABAWS in Apache-Tomcat - simply drop the war file into the\r
-<span class="highlight">webapps</span> directory of a running\r
-Tomcat, and it will do the rest. For any other web application\r
-server, please follow your server's specific deployment procedure\r
-for 'WAR' files. If you are installing on a windows machine, then\r
-at this point your JABAWS installation will already be up and\r
-running, and you can try its services out using the <a href=\r
-"howto.html#usingWsTester">JABAWS test client</a>, but\r
-installations on other operating systems will require a final step\r
-to ensure JABAWS can locate and execute the binary programs it\r
-needs.</p>\r
-\r
-<h4>Preparing executables for use with JABAWS</h4>\r
-\r
-<p>JABAWS's web services use command line programs to do\r
-the actual analysis, so it must have access to programs\r
-which can be executed on your platform. The native executables\r
-bundled with JABAWS for Windows (32-bit) and Linux (i386) should be\r
-OK for those systems. However, the source code for these \r
-programs is also provided so you can recompile for your own\r
-architecture and exploit any optimisations that your system can\r
-provide. Alternately, if you have already got binaries on your\r
-system, then you can simply change the paths in JABAWS's\r
-configuration files so these are used instead.</p>\r
\r
-<h5>Using the pre-compiled i386 binaries on Linux</h5>\r
-\r
-<p>Before the binaries that are bundled with JABAWS can be used,\r
-they must first be made executable using the provided <a name=\r
-"setexecflag" id="setexecflag">'setexecflag.sh'</a> script:</p>\r
+<h2 id="headtitle">JABAWS MANUAL</h2>\r
+<h2>Quick Start Guide</h2>\r
\r
+<h3><a name="whichjaba" id="whichjaba"></a>Choose JABAWS distribution</h3>\r
+<p>There are three main packages you could use</p>\r
<ol>\r
-<li>cd to <span class=\r
-"hightlight"><webapplicationpath>/binaries/src</span></li>\r
-\r
-<li>run <span class="hightlight">sh setexecflag.sh</span></li>\r
-\r
-<li>Make sure binaries supplied work under your OS.<br />\r
- For this run each binary, without any command line options or\r
-input files. If you see an error message complaining about missing\r
-libraries or other problems, then you probably need to <a href=\r
-"#recompbinaries">recompile the binaries</a>. with</li>\r
-\r
-<li>Restart the Tomcat.</li>\r
+ <li>A JABAWS Server Virtual Appliance (or Virtual Machine) - for anyone who wants to run JABAWS locally for themselves </li>\r
+ <li>A JABAWS Server Web Application Archive (WAR) package - for anyone who wants to run JABAWS for their group, lab or organization. Wants to use the cluster or perform very large tasks </li>\r
+ <li>A client package - for anyone who wants to use JABAWS from their own code, without Jalview, scripting against local or public version of JABAWS Server. </li>\r
</ol>\r
-\r
-That's it! JABAWS should work at this point. Try it out using the<a\r
-href="howto.html#usingWsTester">JABAWS test client</a>. If not,\r
-read on... or have a look at <a href=\r
-"howto.html#usingtomcat">deploying on Tomcat</a> tips.<br />\r
- <em>Note: You may want to enable logging, <a href="#logfiles">see\r
-below for instructions on how to do that</a>.</em><br />\r
- \r
-\r
-<h5><a name="recompbinaries">Recompiling the bundled\r
-programs for your system</a></h5>\r
-\r
-<p>If you have a fully equipped build environment on your\r
-(POSIX-like) system, then you should be able to recompile the\r
-programs from the source distributions which are included\r
-in the JABAWS war file. A script called 'compilebin.sh' is provided\r
-to automate this task.</p>\r
-\r
+<p>Virtual Appliance (VA) package (1) contains TurnKey Linux with JABAWS installed. JABAWS VA contains JABAWS WAR deployed on the Apache Tomcat 6 web application server. If you use MS Windows read no further - the VA is the way to go. You would need to install <a href="http://www.vmware.com/products/player">VMWare Player</a> or <a href="http://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox</a> (both are free) on your computer to use this package. More details about JABAWS virtual appliance is available from the <a href="man_servervm.html">Server VA</a> section of the manual. </p>\r
+<p>Option 2, Web Application Archive package contains JABAWS ready to be deployed on the Servlet 2.4 compatible web application server such as Apache Tomcat version 6. To make this version work you would need </p>\r
<ol>\r
-<li>In a terminal window, change the working directory to <span\r
-class="hightlight">binaries/src</span></li>\r
-\r
-<li>execute the <span class="highlight">compilebin.sh</span>\r
-script,<br />\r
- either use: <span class="hightlight">chmod +x compilebin.sh;\r
-compilebin.sh > compilebin.out;</span><br />\r
- or: <span class="hightlight">sh compilebin.sh >\r
-compilebin.out</span></li>\r
-\r
-<li>Now run <span class="hightlight">sh setexecflag.sh</span><br />\r
- If any of the binaries was not recompiled, then a 'file not found'\r
-error will be raised.</li>\r
-\r
-<li>Finally, restart your tomcat (or servlet container), and use\r
-the <a href="howto.html#usingWsTester">JABAWS test client</a> to\r
-check that JABAWS can use the new binaries.</li>\r
+ <li>Install Apache-Tomcat or similar web application server. </li>\r
+ <li>If you are not on Linux, you would have to make binaries for your system available to JABAWS. </li>\r
+ </ol>\r
+<p>Read more on <a href="man_serverwar.html">JABAWS WAR in the manual</a>. </p>\r
+<p>A client only package (3) contains the JABAWS command line client. It functionality is equivalent to that of Jalview . This is the package for anyone who wants to connect to and to use JABAWS from their own software. Read more about how to use command line client <a href="#cmdclient">in the CMD Client</a> section of the manual. Also, JABA Web Services are fully WS-I compliant, so one could use any language to access them. </p>\r
+<p><strong>If you chose option 1 </strong></p>\r
+<p>and you work on Windows or Linux or Unix </p>\r
+<ul>\r
+ <li>download and install VMWare Player </li>\r
+ <li>Download JABAWS Virtual Appliance </li>\r
+ <li>Unpack JABAWS virtual appliance and open it with VMware Player. </li>\r
+ </ul>\r
+<p>otherwise </p>\r
+<ul>\r
+ <li>download and install Virtual Box. </li>\r
+ <li>Download JABAWS Virtual Appliance </li>\r
+ <li>Unpack JABAWS virtual appliance, import it into VirtualBox and then start the appliance. </li>\r
+ </ul>\r
+<p><strong>If you chose option 2 </strong></p>\r
+<p>If you are on Linux or Windows </p>\r
+<ol><li>Download JABAWS WAR </li>\r
+ <li>Download and install <a href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> </li>\r
+ <li>Drop the JABAWS war file into<span class="hightlight"> tomcat/webapps</span> directory. </li>\r
+ <li>If you are on Linux, <span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./setexecflag.sh </span> script to set an executable flag for JABAWS binaries. </li>\r
+ <li>Restart the Tomcat </li>\r
</ol>\r
-\r
-<p>If you couldn't compile everthing, then it may be that your system does\r
-not have all the tools required for compiling the programs. At the very\r
-least check that you have gcc, g++ and make installed in your\r
-system. If not install these packages and repeat the compilation\r
-steps again. You should also review the compilebin.sh output -\r
-which was redirected to compilebin.out, and any errors output to\r
-the terminal. Finally, try obtaining the <a href="#obtainexec">pre\r
-compiled binaries</a> for your OS.</p>\r
-\r
-<h5><a name="haveexec" id="haveexec">Reuse the binaries that are\r
-already in your system</a></h5>\r
-\r
-<p>If you would like to use the binaries you already have then you\r
-just need to let JABAWS know there they are. To do this, edit:\r
-<span class="code">conf/Executable.properties</span>\r
-<p>When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside <span class="highlight">webapps</span>. For example, the default path for clustalw is defined\r
-as<span class=\r
-"code">local.clustalw.bin=binaries/src/clustalw/src/clustalw2</span>\r
-Alternatively, instead of changing <span class=\r
-"hightlight">Executable.properties</span> you could also replace\r
-the executables bundled with JABAWS with the ones that you have, or make symlinks to them.\r
-Then the default configuration will work for you. More information\r
-about <a href="#exec"><span class="hightlight">the\r
-Executable.properties</span> file is given below</a>.</p>\r
-\r
-<h5><a name="obtainexec" id="obtainexec">Obtaining alignment\r
-programs for your operation system from elsewhere</a></h5>\r
-\r
-<p>You could search for pre-packaged compiled executable in your\r
-system package repository or alternately, download pre-compiled\r
-binaries from each alignment program's home page. Then, either\r
-replace the executables supplied with the downloaded ones, or\r
-modify the paths in <span class=\r
-"hightlight">executable.properties</span> as described above.</p>\r
-\r
-<h4>Configuring JABAWS</h4>\r
-\r
-<p>There are three parts of the system you can configure. The local\r
-and cluster engines, and the paths to individual executables for\r
-each engine. These settings are stored in configuration files\r
-within the web application directory (for an overview, then take a\r
-look at the <a href="#warfile">war file content table</a>).</p>\r
-\r
-<h5>Default JABA Web Services Configuration</h5>\r
-\r
-<p>Initially, JABAWS is configured with only the local engine\r
-enabled, with job output written to directory called "jobsout"\r
-within the web application itself. This means that JABAWS will work\r
-out of the box, but may not be suitable for serving a whole lab or\r
-instute.</p>\r
-\r
-<h4>Local Engine Configuration</h4>\r
-\r
-<p>The Local execution engine configuration is defined in the\r
-properties file conf/Engine.local.properties. The supported\r
-configuration settings are:<br />\r
- <span class="hightlight">engine.local.enable=true</span> - #\r
-enable or disable local engine, valid values true | false<br />\r
- <span class=\r
-"hightlight">local.tmp.directory=D:\\clusterengine\\testoutput</span>\r
-- a directory to use for temporary files storage, optional,\r
-defaults to java temporary directory<br />\r
- <span class="hightlight">engine.local.thread.number=4</span> -\r
-Number of threads for tasks execution (valid values between 1 and\r
-2x cpu. Where x is a number of cores available in the system).\r
-Optional defaults to the number of cores for core number <=4 and\r
-number of cores-1 for greater core numbers.</p>\r
-\r
-<p>If you are planning to heavily use the local engine (which you\r
-have to if you do not have a cluster) it is a good idea to increase\r
-the amount of memory available for the web application server. If\r
-you are using Apache-Tomcat, then you can define its memory\r
-settings in the JAVA_OPTS environment variable. To specify which\r
-JVM to use for Apache-Tomcat, put the full path to the JRE\r
-installation in the JAVA_HOME environment variable (We would\r
-recommend using Sun Java Virtual Machine (JVM) in preference to\r
-Open JDK). Below is an example of code which can be added to <span\r
-class="hightlight"><tomcat_dir>/bin/setenv.sh</span> script\r
-to define which JVM to use and a memory settings for Tomcat server.\r
-Tomcat server startup script (<span class=\r
-"hightlight">catalina.sh</span>) will execute <span class=\r
-"hightlight">setenv.sh</span> on each server start\r
-automatically.<br />\r
- <span class="code">export\r
-JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/<br />\r
- export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"</span></p>\r
-\r
-<h4>Cluster Engine Configuration</h4>\r
-\r
-<p>Supported configuration settings:<br />\r
- <span class="hightlight">engine.cluster.enable=true</span> - #\r
-enable or disable local engine true | false, defaults to\r
-false<br />\r
- <span class=\r
-"hightlight">cluster.tmp.directory=/homes/clustengine/testoutput-</span>\r
-a directory to use for temporary files storage. The value must be\r
-an absolute path to the temporary directory. Required. The value\r
-must be different from what is defined for local engine. This\r
-directory must be accessible from all cluster nodes.<br />\r
- For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH\r
-environment variables have to be defined. They tell the cluster\r
-engine where to find DRMAA libraries. These variables\r
-should be defined when the web application server starts up, e.g.</p>\r
-\r
-<p><span class="code">SGE_ROOT=/gridware/sge<br />\r
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
-\r
-<p>Finally, do not forget to configure executables for the cluster\r
-execution, they may be the same as for the local execution but may\r
-be different. Please refer to the executable configuration section\r
-for further details.</p>\r
-\r
-<h4><a name="exec" id="exec"></a>Executable Configuration</h4>\r
-\r
-<p>All the executable programs\r
-are configured in conf/Executable.properties file. Each executable\r
-is configured with a number of options. They are: <span class=\r
-"code">local.X.bin.windows=<path to executable under windows\r
-system, optional><br />\r
- local.X.bin=<path to the executable under non-windows system,\r
-optional><br />\r
- cluster.X.bin=<path to the executable on the cluster, all\r
-cluster nodes must see it, optional><br />\r
- X.bin.env=<semicolon separated list of environment variables\r
-for executable, use hash symbol as name value separator,\r
-optional><br />\r
- X.--aamatrix.path=<path to the directory containing\r
-substitution matrices, optional><br />\r
- X.presets.file=<path to the preset configuration file, optional\r
-><br />\r
- X.parameters.file=<path to the parameters configuration file,\r
-optional><br />\r
- X.limits.file=<path to the limits configuration file,\r
-optional><br />\r
- X.cluster.settings=<list of the cluster specific options,\r
-optional></span></p>\r
-\r
-<p>Where X is a short executable wrapper class name.</p>\r
-\r
-<p>Default JABAWS configuration includes path to local executables\r
-to be run by the local engine only, all cluster related settings\r
-are commened out, but they are there for you as example. Cluster\r
-engine is disabled by default. To configure executable for cluster\r
-execution uncomment the X.cluster settings and change them\r
-appropriately.<br />\r
- For example a complete Mafft configuration may look like\r
-this:<span class="code">local.mafft.bin.windows=<br />\r
- local.mafft.bin=binaries/mafft<br />\r
- cluster.mafft.bin=/homes/cengine/mafft<br />\r
- mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;<br />\r
- mafft.--aamatrix.path=binaries/matrices<br />\r
- mafft.presets.file=conf/settings/MafftPresets.xml<br />\r
- mafft.parameters.file=conf/settings/MafftParameters.xml<br />\r
- mafft.limits.file=conf/settings/MafftLimits.xml<br />\r
- mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l\r
-h_vmem=6000M -l ram=6000M</span></p>\r
-\r
-<p>Please not that relative paths must only be specified for the\r
-files that reside inside web application directory, all other paths\r
-must be supplied as absolute!</p>\r
-\r
-<p>Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly\r
-specify the absolute path to anything\r
-normally evaluated from an environment variable at execution time.</p>\r
-\r
-<p>If you are using JABAWS to submit jobs to the cluster (with\r
-cluster engine enabled), executables must be available from all\r
-cluster nodes the task can be sent to, also paths to the\r
-executables on the cluster e.g. <span class=\r
-"hightlight">cluster.<exec_name>.bin</span> must be\r
-absolute.</p>\r
-\r
-<p>Executables can be located anywhere in your system, they do not\r
-have to reside on the server as long as the web application server\r
-can access and execute them.</p>\r
-\r
-<p>Cluster settings are treated as a black box, the system will\r
-just pass whatever is specified in this line directly to the\r
-cluster submission library. This is how DRMAA itself treats this\r
-settings. More exactly DRMAA JobTemplate.setNativeSpecification()\r
-function will be called.</p>\r
-\r
-<h5><a name="setexecenv" />Defining Environment Variables for\r
-Executables</h5>\r
-\r
-<p>Environment variables can be defined in property <span class=\r
-"code">x.bin.env</span> Where <span class="hightlight">x</span> is\r
-one of five executables supported by JABAWS. Several environment\r
-variables can be specified in the same line. For example.<br />\r
- <span class=\r
-"code">mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;</span></p>\r
-\r
-<p>The example above defines two environment variables with names\r
-MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft\r
-and /bin/fasta34 respectively. Semicolon is used as a separator\r
-between different environment variables whereas hash is used as a\r
-separator for name and value of the variable.</p>\r
-\r
-<h4><a name="mafftconf" id="mafftconf"></a>Configure JABAWS to Work\r
-with Mafft</h4>\r
-\r
-<p>If you use default configuration you do not need to read any\r
-further. The default configuration will work for you without any\r
-changes, however, if you want to install Mafft yourself then there\r
-is a couple of more steps to do.</p>\r
-\r
-<p>Mafft executable needs to know the location of other files\r
-supplied with Mafft. In addition some Mafft functions depends on\r
-the fasta executable, which is not supplied with Mafft, but is a\r
-separate package. Mafft needs to know the location of fasta34\r
-executable.</p>\r
-\r
-<p>To let Mafft know where the other files from its package are\r
-change the value of MAFFT-BINARIES environment variables. To let\r
-Mafft know where is the fasta34 executable set the value of\r
-FASTA_4_MAFFT environment variable to point to a location of\r
-fasta34 program. The latter can be added to the PATH variable\r
-instead. If you are using executables supplied with JABAWS, the\r
-path to Mafft binaries would be like <span class=\r
-"hightlight"><relative path to web application\r
-directory>/binaries/src/mafft/binaries</span> and the path to\r
-fasta34 binary would be <span class="hightlight"><relative path\r
-to web application\r
-directory>/binaries/src/fasta34/fasta34</span>. You can specify\r
-the location of Mafft binaries as well as fasta34 program elsewhere\r
-by providing an absolute path to them. All these settings are\r
-defined in <span class=\r
-"hightlight">conf/Executable.properties</span> file.</p>\r
-\r
-<h4>Testing JABA Web Services</h4>\r
-\r
-<p>You can use a command line client (part of the client only\r
-package) to test you JABAWS installation as described <a href=\r
-"howto.html#usingcclient">here</a>. If you downloaded a JABAWS\r
-server package, you can use <span class=\r
-"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span>\r
-to test JABAWS installation as described in <a href=\r
-"howto.html#usingWsTester">how-to</a>. If you downloaded the source\r
-code, then you could run a number of test suits defined in the\r
-build.xml ant build file.</p>\r
-\r
-<h4><a name="logfiles" id="logfiles"></a>JABAWS Log Files</h4>\r
-\r
-<p>JABAWS can be configured to log what it is doing. This comes\r
-handy if you would like to see who is using your web services or\r
-need to chase some problems. JABAWS uses <a href=\r
-"http://logging.apache.org/log4j/1.2/">log4j</a> to do the logging,\r
-the example of log4j configuration is bundled with JABAWS war file.\r
-You will find it in the <span class=\r
-"hightlight">/WEB-INF/classes/log4j.properties</span> file. All the\r
-lines in this file are commented out. The reason why the logging is\r
-disabled by default it simple, log4j have to know the exact\r
-location where the log files should be stored. This is not known up\r
-until the deployment time. To enable the logging you need to\r
-define<span class="hightlight">logDir</span> property in the <span\r
-class="hightlight">log4j.properties</span> and uncomment section of\r
-the file which corresponds to your need. More information is given\r
-in the <span class="hightlight">log4j.properties</span> file\r
-itself. Restart the tomcat or the JABAWS web application to apply\r
-the settings.</p>\r
-\r
-<p>After you have done this, assuming that you did not change the\r
-log4j.properties file yourself, you should see the application log\r
-file called <span class="hightlight">activity.log</span>. The\r
-amount of information logged can be adjusted using different\r
-logging levels, it is reduced in the following order of log levels\r
-TRACE, DEBUG, INFO, WARN, ERROR, FATAL.</p>\r
-\r
-<p>If you would like to know who is using your services, you might\r
-want to <a href="howto.html#logs">enable tomcat access\r
-logging</a>.</p>\r
-\r
-<h4><a name="warfile" id="warfile"></a>JABAWS War File Content</h4>\r
-\r
-<table width="100%">\r
-<tr>\r
-<th width="19%">Directory</th>\r
-<th width="81%">Content description</th>\r
-</tr>\r
-\r
-<tr>\r
-<td>conf/</td>\r
-<td>contains configuration files such as Executable.properties,\r
-Engine.local.properties, Engine.cluster.properties</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>conf/settings</td>\r
-<td>Contains individual executable description files. In particular\r
-XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the\r
-name of the executable</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>jobsout/</td>\r
-<td>Contains directories generated when running an individual executable. E.g. input and output files and some other task\r
-related data. (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/</td>\r
-<td>Directory contains native executables - programs,\r
-windows binaries (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/src</td>\r
-<td>Contains source of native executables and Linux i386\r
-binaries.</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/matrices</td>\r
-<td>Substitution matrices <!-- what format ? --></td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF</td>\r
-<td>Web application descriptor</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF/lib</td>\r
-<td>Web application libraries</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF/classes</td>\r
-<td>log4j.properties - log configuration file (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td colspan="2"><strong>Help Pages</strong> </td>\r
-</tr>\r
-\r
-<tr>\r
-<td>/</td>\r
-<td>help pages, index.html is the starting page</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>dm_javadoc</td>\r
-<td>javadoc for JABAWS client (the link is available from How To\r
-pages)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>prog_docs</td>\r
-<td>documentation for programmes that JABAWS uses</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>images</td>\r
-<td>images referenced by html pages</td>\r
-</tr>\r
-</table>\r
-\r
-<p> </p>\r
-</div>\r
-\r
-<!-- content end-->\r
-<div id="copyright">Last update: 19 August 2010<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\r
-<!-- wrapper end-->\r
+<p>otherwise</p>\r
+<ul>\r
+ <li>Complete steps 1-3 from the above.</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
+ <li>Restart the Tomcat </li>\r
+</ul>\r
+<p>Once you have JABAWS working you can point the Jalview to your local JABAWS. </p>\r
+<ul>\r
+ <li>Download and start the desktop version of <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a> </li>\r
+ <li>Go to Jalview->Tools->Preferences->Webservices->New Service URL and enter the JABAWS URL which you can see one your appliance is booted up. </li>\r
+</ul>\r
+<p><strong>if you chose option 3</strong> </p>\r
+<p>You can use the client straight out of the box. </p>\r
+</div> \r
+<!-- about end-->\r
</div>\r
-<!-- page end-->\r
+<!-- content end--> \r
+<div id="copyright">Last update: 7 January 2011<br/>\r
+Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+</div><!-- wrapper end-->\r
+</div> <!-- page end-->\r
\r
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