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 174   <div class="section" id="command-line-client-cli">
 175 <h1>Command Line Client (CLI)<a class="headerlink" href="#command-line-client-cli" title="Permalink to this headline">¶</a></h1>
 176 <p>The JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web services. This 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. The JABA Web Services are <a class="reference external" href="http://www.ws-i.org/">WS-I</a> compliant. This means that you can access them from any language that has libraries or functions for consuming interoperable SOAP web services. More information on how to develop software that access JABAWS services is provided in the <a class="reference external" href="develop.html#accessing-jabaws-from-your-program">documentation pages</a>.</p>
 177 <p>The command line client comes as a part of <a class="reference external" href="../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 class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/full_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>
 178 <hr class="docutils" />
 179 <div class="section" id="installing">
 180 <span id="client-installing"></span><h2>Installing<a class="headerlink" href="#installing" title="Permalink to this headline">¶</a></h2>
 181 <div class="admonition tip">
 182 <p class="first admonition-title">Tip</p>
 183 <p class="last">Check if you are running the recommended version of Java.</p>
 184 </div>
 185 <p>You need Java 7 or higher installed in your machine to be able to run the JABAWS CLI client.
 186 Please see the <cite>Java</cite> web site for up to date instructions and downloads.</p>
 187 <hr class="docutils" />
 188 </div>
 189 <div class="section" id="usage">
 190 <span id="cli-usage"></span><h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
 191 <div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span>
 192 </pre></div>
 193 </div>
 194 <div class="highlight-default"><div class="highlight"><pre><span></span>Usage:
 195 java -jar &lt;path_to_jar_file&gt; -h=host_and_context -s=serviceName ACTION [OPTIONS]
 196 -h=&lt;host_and_context&gt; - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
 197 -s=&lt;ServiceName&gt; - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
 198
 199
 200 ACTIONS:
 201 -i=&lt;inputFile&gt; - full path to fasta formatted sequence file, from which to align sequences
 202 -parameters - lists parameters supported by web service
 203 -presets - lists presets supported by web service
 204 -limits - lists web services limits
 205 Please note that if input file is specified other actions are ignored
 206
 207
 208  OPTIONS: (only for use with -i action):
 209 -r=&lt;presetName&gt; - name of the preset to use
 210 -o=&lt;outputFile&gt; - full path to the file where to write an alignment
 211 -f=&lt;parameterInputFile&gt; - the name of the file with the list of parameters to use.
 212
 213 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!
 214 </pre></div>
 215 </div>
 216 <hr class="docutils" />
 217 </div>
 218 <div class="section" id="example-usage">
 219 <span id="cli-example"></span><h2>Example Usage<a class="headerlink" href="#example-usage" title="Permalink to this headline">¶</a></h2>
 220 <p>Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console.</p>
 221 <div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span>
 222 </pre></div>
 223 </div>
 224 <p>Content of input.fasta file is show below (please note sequences has been trimmed for clarity)</p>
 225 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">&gt;</span><span class="n">Foobar</span>
 226 <span class="n">MTADGPRELLQLRAAVRHRPQDFVAWL</span>
 227 <span class="o">&gt;</span><span class="n">Bar</span>
 228 <span class="n">MGDTTAGEMAVQRGLALHQ</span>
 229 <span class="o">&gt;</span><span class="n">Foofriend</span>
 230 <span class="n">MTADGPRELLQLRAAV</span>
 231 </pre></div>
 232 </div>
 233 <p>Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file</p>
 234 <div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span>  <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span> <span class="o">-</span><span class="n">o</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="n">out</span><span class="o">.</span><span class="n">clustal</span> <span class="o">-</span><span class="n">f</span><span class="o">=</span><span class="n">prm</span><span class="o">.</span><span class="ow">in</span>
 235 </pre></div>
 236 </div>
 237 <p>The content of the prm.in file is shown below</p>
 238 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">nofft</span>
 239 <span class="o">--</span><span class="n">noscore</span>
 240 <span class="o">--</span><span class="n">fastaparttree</span>
 241 <span class="o">--</span><span class="n">retree</span><span class="o">=</span><span class="mi">10</span>
 242 <span class="o">--</span><span class="n">op</span><span class="o">=</span><span class="mf">2.2</span>
 243 </pre></div>
 244 </div>
 245 <p>The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equals sign. This format is constant no matter which JABAWS web service is used.</p>
 246 <div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">parameters</span>
 247 </pre></div>
 248 </div>
 249 <p>The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key.</p>
 250 <p>For example you used <code class="docutils literal"><span class="pre">-h=http://myhost.compbio.ac.uk:8080/jabaws</span></code> server, now you want to use another server to <code class="docutils literal"><span class="pre">-h=http://mylabserver.myuni.edu</span></code>. This comes handy if your favorite server is off and you need to do the job yesterday.</p>
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