<!--<h4>About</h4>-->
<ul>
<li><a href="#wisjaba">What is JABAWS?</a></li>
+ <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="#wjaba">JABAWS Benefits</a></li>
- <li><a href="#alprog">JABA Web Services Programs</a></li>
+ <li><a href="#alprog">Bioinformatics tools included in JABAWS</a></li>
<li><a href="#jaba2.2">What is new in JABAWS 2.2?</a> </li>
- <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
</ul>
JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a
collection of web services for bioinformatics, and currently provides services that make it easy
to access well-known multiple sequence alignment and protein disorder prediction programs
- (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.
+ (see <a href="#alprog">the list of currently supported programs</a>).
Future versions of JABAWS will incorporate other tools.
</p>
<strong>Getting JABAWS</strong>
<p>
- JABAWS consists of a server and a 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
+ JABAWS consists of a server and a 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
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>.
+ It requires no configuration and is simple to install. If you want to install JABAWS for your
+ lab or institution then download the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>.
+ 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.
+ in writing your own client, the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a> is what you need.
+ </p>
+ <p class="text-right">
+ <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
+ </p>
+ </div>
+ </div>
+ </div>
+</div>
+<div class="row" id="jabaclient">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">What is the JABAWS Client?</h1>
+ </div>
+ <div class="panel-body">
+ <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
+ services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
+ services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
+ to test or execute the programs provided by the JABAWS server in your own scripts, but you do not want to handle
+ any web service specific details. The client is an open source software, so you can also use the source code to
+ as an example how to manipulate with JABAWS web services in your own code.
+ <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
+ example of a graphical JABAWS client. This client uses the same functionality as the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a>, but
+ instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
</div>
<div class="panel-body">
<ul>
- <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
+ <li>Can be deployed on most operating systems, as a VMware or compatible Virtual Appliance, as well as a Tomcat Java Web Application.</li>
<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
<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>
<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>
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">JABA Web Services Programs</h1>
+ <h1 class="panel-title">Bioinformatics tools included in JABAWS</h1>
</div>
<div class="panel-body">
<p>JABAWS currently provides access to the following programs:</p>
</div>
<div class="panel-body">
- <strong>JABAWS Version 2.2 (Released XX Feb 2017)</strong>
+ <strong>JABAWS Version 2.2 (Released XX March 2017)</strong>
<p >The website was improved and several service programs were update:</p>
<ul>
<li>The versions of several application programs provided by JABAWS were bumped to the latest available.
The pre-configured JABAWS Amazon Machine Image (AMI),
which allowed for JABAWS to be run
in the <a href="http://aws.amazon.com/what-is-aws">Amazon EC2 cloud</a>, is no longer provided
- due to very limited use by the scientific community.
+ due to very limited use by the scientific community peers.
</li>
</ul>
</div>
</div>
</div>
-<div class="row" id="jabaclient">
- <div class="col-md-12">
- <div class="panel panel-default">
- <div class="panel panel-heading">
- <h1 class="panel-title">What is the JABAWS Client?</h1>
- </div>
- <div class="panel-body">
- <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
- services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
- services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
- to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle
- any web service specific details. The client is an open source software, so you can also use the source code to
- as an example how to manipulate with JABAWS web services in your own code.
- <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
- example of a graphical JABAWS client. This client uses the same functionality as the command line client, but
- instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
- </p>
- <p class="text-right">
- <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
- </p>
- </div>
- </div>
- </div>
-</div>
<div class="row" id="jalviewsup">
<div class="col-md-12">
<div class="panel panel-default">
<li><a href="man_docs.jsp">Documentation</a></li>
<li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
</ol>
-<div class="row" id="usingcclient">
+<div class="row">
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">JABAWS Command Line Client Usage</h1>
+ <h1 class="panel-title">Command Line Client</h1>
+ </div>
+ <div class="panel-body">
+ <!--<h4>About</h4>-->
+ <ul>
+ <li><a href="#usingcclient1">Overview of the Command Line Client</a></li>
+ <li><a href="#usingcclient2">Command Line Client Usage</a></li>
+ <li><a href="#usingcclient3">Example Usage</a></li>
+ </ul>
+ <!--<p class="justify">-->
+ <!--</p>-->
+ </div>
+ </div>
+ </div>
+</div>
+<div class="row" id="usingcclient1">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">Overview of the Command Line Client</h1>
</div>
<div class="panel-body">
<p class="justify">
The command line client comes as a part of
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download"> client package</a>
+ <a href="${pageContext.request.contextPath}/download.jsp#client">client package</a>
which you are welcome to download.
The command line client can be used to align sequences using any of JABAWS supported web
services. The client is OS independent and supports most of
the functions which can be accessed programmatically via
- <a href="dm_javadoc/index.html">JABAWS API</a>. Using this client you could align sequences
+ <a href="${pageContext.request.contextPath}/full_javadoc/">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>
+ </div>
+ </div>
+ </div>
+</div>
+<div class="row" id="usingcclient2">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">Command Line Client Usage</h1>
+ </div>
+ <div class="panel-body">
+ <pre><code class="bash">java -jar jaba-client.jar</code></pre>
<pre><strong>Usage:</strong>
java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
-o=<outputFile> - full path to the file where to write an alignment
-f=<parameterInputFile> - the name of the file with the list of parameters to use.<br />
Please note that -r and -f options cannot be used together. Alignment is done with either preset or aparameters from the file, but not both!</pre>
-
+ </div>
+ </div>
+ </div>
+</div>
+<div class="row" id="usingcclient3">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">Example Usage</h1>
+ </div>
+ <div class="panel-body">
<p class="justify">
Align sequences from input.fasta file using Mafft web
service with default settings, print alignment in Clustal format to console.
<em2>-h=http://mylabserver.myuni.edu.</em2> This comes handy if
your favorite server is off and you need to do the job yesterday.
</p>
-
</div>
</div>
</div>
<ol class="breadcrumb">
<li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
<li><a href="man_docs.jsp">Documentation</a></li>
- <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
+ <li class="active"><a href="man_server_dev.jsp">Configuring JABAWS</a></li>
</ol>
<div class="row">
<div class="col-md-12">
<li><a href="#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>
<li><a href="#diffbin">Using a different version of the alignment program with JABAWS</a></li>
<li><a href="#mixuse">Load balancing </a></li>
- <li><a href="#testingJaba">Testing JABA Web Services</a></li>
+ <li><a href="#testingJaba">Testing JABAWS Web-Services</a></li>
<li><a href="#logs">JABAWS requests logging </a></li>
<li><a href="#logfiles">JABAWS internal logging </a></li>
<li><a href="#warfile">JABAWS War File Content</a></li>
</p>
<pre><code class="bash">local.X.bin.windows=<path to executable under windows system, optional>
local.X.bin=<path to the executable under non-windows system, optional>
-cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional><
+cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional>
X.bin.env=<semicolon separated list of environment variables for executable, use hash symbol as name value separator, optional>
X.--aamatrix.path=<path to the directory containing substitution matrices, optional>
X.presets.file=<path to the preset configuration file, optional>
X.limits.file=<path to the limits configuration file, optional>
X.cluster.settings=<list of the cluster specific options, optional></code></pre>
- <p>Where X is either clustal, muscle, mafft, probcons or tcoffee.</p>
+ <p>Where X any of the bioinformatics tools available (e.g. clustalw, muscle, mafft, probcons, t-coffee, etc.).</p>
<p class="justify">
Default JABAWS configuration includes path to local executables
<p>Environment variables can be defined in property</p>
<pre><code class="bash">x.bin.env</code></pre>
<p>
- Where <em2>x</em2> is one of five executables supported by JABAWS. Several environment
+ Where <em2>x</em2> is one of thw executables supported by JABAWS. Several environment
variables can be specified in the same line. For example.
</p>
<pre><code class="bash">mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;</code></pre>
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">Testing JABA Web Services</h1>
+ <h1 class="panel-title">Testing JABAWS Web-Services</h1>
</div>
<div class="panel-body">
<p class="justify">
<td>log4j.properties - log configuration file (optional)</td>
</tr>
<tr>
+ <td>static</td>
+ <td>Static content such as CSS, JavaScript and Image files</td>
+ </tr>
+ <tr>
<td colspan="2"><strong>Help Pages</strong> </td>
</tr>
<tr>
</tr>
<tr>
<td>dm_javadoc</td>
- <td>javadoc for JABAWS client (the link is available from How To
- pages)</td>
+ <td><a href="${pageContext.request.contextPath}/dm_javadoc/">JavaDoc for the JABAWS Data Model</a></td>
</tr>
<tr>
- <td>prog_docs</td>
- <td>documentation for programs that JABAWS uses</td>
+ <td>full_javadoc</td>
+ <td><a href="${pageContext.request.contextPath}/full_javadoc/">JavaDoc for the complete JABAWS</a></td>
</tr>
<tr>
- <td>images</td>
- <td>images referenced by html pages</td>
+ <td>prog_docs</td>
+ <td><a href="${pageContext.request.contextPath}/prog_docs/">Documentation for programs that are included in JABAWS</a></td>
</tr>
+
</table>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
<ol class="breadcrumb">
<li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
<li><a href="man_docs.jsp">Documentation</a></li>
- <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
+ <li class="active"><a href="man_server_dev.jsp">Accessing JABAWS</a></li>
</ol>
<div class="row">
<div class="col-md-12">
</div>
<div class="panel-body">
<p class="justify">
- All JABA multiple sequence alignment web services comply to the same
+ All JABAWS multiple sequence alignment web services comply to the same
interface, thus the function described below are available from all the services.
</p>
<strong>Functions for initiating the alignment </strong>
LimitsManager lm = getLimits()
PresetManager pm = getPresets()</code></pre>
<p class="justify">
- Please refer to a <a href="dm_javadoc/compbio/data/msa/MsaWS.html">data model
- javadoc</a> for a detailed description of each methods.
+ Please refer to a <a href="${pageContext.request.contextPath}/dm_javadoc/compbio/data/msa/MsaWS.html">Data Model
+ JavaDoc</a> for a detailed description of each methods.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
compbio-util-1.3.jar and compbio-annotation-1.0.jar.
</p>
<p class="justify">
- Please refer to a <a href="dm_javadoc/index.html">data model javadoc</a>
+ Please refer to a <a href="${pageContext.request.contextPath}/dm_javadoc/index.html">Data Model JavaDoc</a>
for a detailed description of each class and its methods.
</p>
<p class="text-right">
For a complete working example of JABAWS command line client please see
compbio.ws.client.Jws2Client class. JABAWS command line client
source code is available from the
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev">download page</a>.
+ <a href="${pageContext.request.contextPath}/download.jsp">download page</a>.
Please note that for now all
the examples are in Java, other languages will follow if there is sufficient demand.
</p>
MsaWS specification, thus from the caller point of view all JABAWS web
services can be represented by MsaWS
interface. The full documentation of MsaWS functions is available from
- the <a href="dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>.
+ the <a href="${pageContext.request.contextPath}/dm_javadoc/compbio/data/msa/MsaWS.html">JavaDoc</a>.
</p>
<p class="text-right">
</div>
<div class="panel-body">
<p>Multiple sequence alignment services</p>
- <ul><li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalOWS?wsdl">ClustalOWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalOWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MuscleWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MafftWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/TcoffeeWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ProbconsWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MSAprobsWS?wsdl">MSAprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MSAprobsWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/GLprobsWS?wsdl">GLprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GLprobsWS?wsdl) </li>
+ <ul><li><a href="${pageContext.request.contextPath}/ClustalOWS?wsdl">ClustalOWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalOWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MuscleWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MafftWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/TcoffeeWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ProbconsWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/MSAprobsWS?wsdl">MSAprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MSAprobsWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/GLprobsWS?wsdl">GLprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GLprobsWS?wsdl) </li>
</ul>
<p>Protein disorder prediction services</p>
<ul>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/IUPredWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GlobPlotWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/DisemblWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JronnWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/IUPredWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GlobPlotWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/DisemblWS?wsdl) </li>
+ <li><a href="${pageContext.request.contextPath}/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JronnWS?wsdl) </li>
</ul>
<p>Amino acid conservation service</p>
<ul>
<li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/AAConWS?wsdl">AAConWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/AAConWS?wsdl) </li>
</ul>
- <p>Protein and RNA Secondary Structure Prediction</p>
+ <p>RNA Secondary Structure Prediction</p>
<ul>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl">JpredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl) </li>
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/RNAalifoldWS?wsdl">RNAalifoldWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/RNAalifoldWS?wsdl) </li>
+ <%--<li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl">JpredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl) </li>--%>
+ <li><a href="${pageContext.request.contextPath}/RNAalifoldWS?wsdl">RNAalifoldWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/RNAalifoldWS?wsdl) </li>
</ul>
<p class="justify">
Please replace <em2>http://www.compbio.dundee.ac.uk/</em2> with your JABAWS instance host name, and
<p class="justify">The names of all the parameters supported by a web service e.g. "PAM300" can be obtained
using <em2>options.getArguments()</em2>method. Further details on the methods
available from <em2>RunnerConfig</em2> object are available from the
- <a href="dm_javadoc/index.html">javadoc</a>.
+ <a href="${pageContext.request.contextPath}/dm_javadoc/index.html">JavaDoc</a>.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
<p class="justify">
Finally, a complete example of the program that connects to JABAWS Clustal
service and aligns sequences using
- one of the Clustal web service presets. There is also a
- <a href="2.1/Example_template.pdf">PDF version</a> of
- this example with syntax highlighted. The text comments are commented by block
- style comments e.g. /* comment */,
- the alternatives given in the code are line commented // comment. You may want
- to remove line style comments to
- test alternatives of the functions. All you need for this to work is a
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=min-jaba-client-2.0.jar">JABAWS binary client</a>.
+ one of the Clustal web service presets. All you need for this to work is a
+ <a href="${pageContext.request.contextPath}/download.jsp#client">JABAWS binary client</a>.
Please make sure that the client is in the Java class path before running this example.
</p>
<pre><code class="java">
}
</code></pre>
<p>For a more detailed description of all available types and their functions please
- refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
+ refer to the <a href="dm_javadoc/index.html">Data Model JavaDoc</a>.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
<a href="man_about.jsp">What is JABAWS?</a>
<ul>
<li><a href="man_about.jsp#wisjaba">What is JABAWS?</a></li>
+ <li><a href="man_about.jsp#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="man_about.jsp#wjaba">JABAWS Benefits</a></li>
- <li><a href="man_about.jsp#alprog">JABA Web Services Programs</a></li>
+ <li><a href="man_about.jsp#alprog">Bioinformatics tools included in JABAWS</a></li>
<li><a href="man_about.jsp#jaba2.2">What is new in JABAWS 2.2?</a> </li>
- <li><a href="man_about.jsp#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="man_about.jsp#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
<li><a href="man_about.jsp#cmdclient">Programmatic access to JABAWS</a></li>
</ul>
<ul>
<li><a href="man_serverwar.jsp#sysreq">System Requirements</a></li>
<li><a href="man_serverwar.jsp#instwar">Installing the JABAWS WAR file</a></li>
- <li><a href="man_serverwar.jsp#prepexec">Preparing executables for use with JABAWS</a></li>
+ <li><a href="man_serverwar.jsp#prepexec">Preparing executables to use with JABAWS</a></li>
<li><a href="man_serverwar.jsp#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>
<li><a href="man_serverwar.jsp#recompbinaries">Recompiling the bundled programs for your system</a></li>
<li><a href="man_serverwar.jsp#haveexec">Reuse the binaries that are already in your system</a></li>
<br/>
<li>
<a href="man_client.jsp">Command Line Client</a>
+ <ul>
+ <li><a href="man_client.jsp#usingcclient1">Overview of the Command Line Client</a></li>
+ <li><a href="man_client.jsp#usingcclient2">Command Line Client Usage</a></li>
+ <li><a href="man_client.jsp#usingcclient3">Example Usage</a></li>
+ </ul>
</li>
<br/>
<li>
<li><a href="man_configuration.jsp#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>
<li><a href="man_configuration.jsp#diffbin">Using a different version of the alignment program with JABAWS</a></li>
<li><a href="man_configuration.jsp#mixuse">Load balancing </a></li>
- <li><a href="man_configuration.jsp#testingJaba">Testing JABA Web Services</a></li>
+ <li><a href="man_configuration.jsp#testingJaba">Testing JABAWS Web-Services</a></li>
<li><a href="man_configuration.jsp#logs">JABAWS requests logging </a></li>
<li><a href="man_configuration.jsp#logfiles">JABAWS internal logging </a></li>
<li><a href="man_configuration.jsp#warfile">JABAWS War File Content</a></li>
</li>
<br/>
<li>
- <a href="man_server_dev.jsp">Develop JABAWS</a>
+ <a href="man_server_dev.jsp">Developing JABAWS</a>
<ul>
<li><a href="man_server_dev.jsp#api">The API</a></li>
<li><a href="man_server_dev.jsp#thesrc">The source code</a></li>
<li><a href="man_server_dev.jsp#projstruct">Structure of the project</a></li>
<li><a href="man_server_dev.jsp#thecode">The code structure</a></li>
<li><a href="man_server_dev.jsp#runtests">Running tests</a></li>
- <li><a href="man_server_dev.jsp#prepexec">Preparing distributive's</a></li>
+ <li><a href="man_server_dev.jsp#prepexec">Preparing distributives</a></li>
<li><a href="man_server_dev.jsp#buildstubs">Building web services artifacts</a></li>
<li><a href="man_server_dev.jsp#addnewws">Adding a new web service (rough guide)</a></li>
</ul>
<li><a href="man_stats.jsp#detailed_usage">Detailed Usage Statistic </a></li>
<li><a href="man_stats.jsp#job_list">Job List</a></li>
<li><a href="man_stats.jsp#job_dir">Single Job Directory Content </a></li>
- <li><a href="man_stats.jsp#conf_tomcat_user">Configuring a privileged access for Tomcat web application server</a></li>
+ <li><a href="man_stats.jsp#conf_tomcat_user">Configuring a privileged
+ access for Tomcat web application server</a></li>
<li><a href="man_stats.jsp#exec_stat_conf">Configuring JABAWS execution statistics</a></li>
</ul>
</li>
<br/>
+ <li>
+ <a href="${pageContext.request.contextPath}/full_javadoc/">Complete JavaDoc</a>
+ </li>
+ <li>
+ <a href="${pageContext.request.contextPath}/dm_javadoc/">Data Model JavaDoc</a>
+ </li>
+ <br/>
</ul>
<!--<p class="justify">-->
<!--</p>-->
<ol class="breadcrumb">
<li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
<li><a href="man_docs.jsp">Documentation</a></li>
- <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
+ <li class="active"><a href="man_server_dev.jsp">Developing JABAWS</a></li>
</ol>
<div class="row">
<div class="col-md-12">
</div>
<div class="panel-body">
<p>This page is for anyone who wants to add a new webservice into the JABAWS framework.</p>
- <p><a href="dm_javadoc/index.html">Data model</a> javadoc- read this if your are coding
+ <p><a href="${pageContext.request.contextPath}/dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding
against JABA Web Services
</p>
- <p><a href="full_javadoc/index.html">Complete</a> javadoc - for developers who want to
+ <p><a href="${pageContext.request.contextPath}/full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to
use JABAWS framework and use Engines and Executables directly
</p>
<p class="text-right">
<h1 class="panel-title">The source code</h1>
</div>
<div class="panel-body">
- <p><a name="svn">Publicly available Git repository:</a>
+ <p><strong>Publicly available Git repository:</strong>
<a href="http://source.jalview.org/gitweb/?p=jabaws.git;a=summary">
http://source.jalview.org/gitweb/?p=jabaws.git;a=summary</a></p>
<p>Another publicly available JABAWS repository, containing the code for each
<p>Several testing groups are supported:</p>
<ul>
- <li>All tests (Test)</li>
- <li>Cluster tests (Run_cluster_dependent_test)</li>
- <li>Cluster independent tests () </li>
- <li>Windows only tests (All_cluster_independent_windows_only_tests) </li>
- <li>Performance and stability tests (Long_tests) </li>
- <li>Re-run failed tests (Rerun_failed_tests) </li>
- <li>Run custom test (CustomTest) </li>
+ <li>All tests ('Test')</li>
+ <li>Cluster tests ('Run_cluster_dependent_test')</li>
+ <li>Cluster independent tests ('All_cluster_independent_tests') </li>
+ <li>Windows only tests ('All_cluster_independent_windows_only_tests') </li>
+ <li>Performance and stability tests ('Long_tests') </li>
+ <li>Re-run failed tests ('Rerun_failed_tests') </li>
+ <li>Run custom test ('CustomTest') </li>
</ul>
<p class="justify">
- To run the tests you need to download all sources from <a href="#svn">repository</a>.
+ To run the tests you need to download all sources from <a href="#thesrc">repository</a>.
Once you have done that, enter into the command line mode, change directory to the
project directory and type:
</p>
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">Preparing distributive's</h1>
+ <h1 class="panel-title">Preparing distributives</h1>
</div>
<div class="panel-body">
<p class="justify">
</div>
<div class="panel-body">
<p class="justify">The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">Virtual Appliance</a> is a
- way to run JABAWS server locally without the need to connect to the internet or configure JABAWS.
+ way to run a JABAWS server locally, without the need to connect to the internet or configure JABAWS.
What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM),
running an installation of the JABAWS Web Application Archive (WAR) on
<a href="http://www.turnkeylinux.org">TurnKey Linux 12.1 (Tomcat edition)</a>. Once this has
<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 with VMware Player v 3.1.2 on Windows and Linux, and
VMware Fusion on Mac.
- However, you are not limited to these virtualization systems and can use the JABAWS appliance with
+ 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.
<h1 class="panel-title">When to use the Virtual Appliance</h1>
</div>
<div class="panel-body">
- <p class="justify">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
+ <p class="justify">The appliance best suits users who would like to use the JABAWS web-services locally.
+ This might be because they do not want to access
systems over an internet, or just want to keep their data private. It is also
- the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run.
+ 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>
<p class="justify">
- For servers that will be used heavily, we recommend that a <a href="man_serverwar.jsp#instwar">JABAWS Server WAR distribution</a> is deployed, rather than the Virtual Appliance version of JABAWS.
+ For servers that will be used heavily, we recommend that a
+ <a href="man_serverwar.jsp#instwar">JABAWS Server WAR distribution</a> is deployed, rather than the
+ Virtual Appliance version of JABAWS.
This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory
- (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to be sufficient for heavy computation.
+ (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to
+ be sufficient for heavy computation.
It is possible to reconfigure the virtual appliance so it uses more computation resources,
- but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine tune to take advantage of the available resources.
+ but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine
+ tune to take advantage of the available resources.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
<ul>
<li><a href="#sysreq">System Requirements</a></li>
<li><a href="#instwar">Installing the JABAWS WAR file</a></li>
- <li><a href="#prepexec">Preparing executables for use with JABAWS</a></li>
+ <li><a href="#prepexec">Preparing executables to use with JABAWS</a></li>
<li><a href="#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>
<li><a href="#recompbinaries">Recompiling the bundled programs for your system</a></li>
<li><a href="#haveexec">Reuse the binaries that are already in your system</a></li>
the <em2>localhost:8080</em2> and
<strong>jaba.war</strong> file is put into the
<em2><tomcat server root>/webapps</em2> directory,
- the deployed application from the jaba.war file then can be accessed by this
- URL http://localhost:8080/<strong>jaba</strong>.
+ the deployed application from the jabaws.war file then can be accessed by this
+ URL http://localhost:8080/<strong>jabaws</strong>.
</p>
<p class="justify">For any other web application
server, please follow your server's specific deployment procedure
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">Preparing executables for use with JABAWS</h1>
+ <h1 class="panel-title">Preparing executables to use with JABAWS</h1>
</div>
<div class="panel-body">
<p class="justify">
</p>
<p class="justify">
You can try the JABAWS functionality with the JABAWS<a
- href="#usingWsTester"> test client</a> or have a look at <a href="http://tomcat.apache.org/tomcat-6.0-doc/deployer-howto.html">deploying on Tomcat</a> tips if you experience any problems.<br />
- <em2>Note: You may want to enable logging,
- <a href="man_configuration.jsp#logfiles"> as described here</a></em2>.
+ href="#usingWsTester"> test client</a> or have a look at
+ <a href="http://tomcat.apache.org/tomcat-7.0-doc/deployer-howto.html">deploying on Tomcat</a>
+ tips if you experience any problems.<br />
+ <em>Note: You may want to enable logging,
+ <a href="man_configuration.jsp#logfiles"> as described here</a></em>.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
symbolic links to them.
Then the default configuration will work for you. More information
about the <em2>Executable.properties</em2> file is given in the
- <a href="man_configuration.jsp#exec">JABAWS Configuration chapter.</a>
+ <a href="man_configuration.jsp#exec">JABAWS Configuration page.</a>
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
<p class="justify">
To stop Tomcat from automatically undeploying your application if the war file is
removed use an explicit application descriptor. It could come in different flavors,
- the one I prefer is to drop a context descriptor file into
+ the one we prefer is to drop a context descriptor file into
<em2><tomcatRoot>conf/Catalina/localhost</em2> directory.
Name your context file the same as your application folder e.g. if your
- JABAWS resides in webappl/jabaws folder, then call the context file jabaws.xml.
+ JABAWS resides in webapps/jabaws folder, then call the context file jabaws.xml.
Below is an example of content this file might have.
</p>
<pre><code class="xml"><?xml version="1.0" encoding="UTF-8"?>
<div class="panel-body">
<p class="justify">
<img src="static/img/usage_statistics_job_details.gif" alt="JABAWS- job details"
- width="716" height="420" /></p>
+ width="600" height="340" /></p>
<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
git://source.jalview.org / jabaws.git / commitdiff