website/man_client.jsp

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  10 <c:import url="template_header.jsp" >
  11     <c:param name="title">Documentation</c:param>
  12 </c:import>
  13
  14 <ol class="breadcrumb">
  15     <li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
  16     <li><a href="man_docs.jsp">Documentation</a></li>
  17     <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
  18 </ol>
  19 <div class="row">
  20     <div class="col-md-12">
  21         <div class="panel panel-default">
  22             <div class="panel panel-heading">
  23                 <h1 class="panel-title">Command Line Client</h1>
  24             </div>
  25             <div class="panel-body">
  26                 <!--<h4>About</h4>-->
  27                 <ul>
  28                     <li><a href="#usingcclient1">Overview of the Command Line Client</a></li>
  29                     <li><a href="#usingcclient2">Command Line Client Usage</a></li>
  30                     <li><a href="#usingcclient3">Example Usage</a></li>
  31                 </ul>
  32                 <!--<p class="justify">-->
  33                 <!--</p>-->
  34             </div>
  35         </div>
  36     </div>
  37 </div>
  38 <div class="row" id="usingcclient1">
  39     <div class="col-md-12">
  40         <div class="panel panel-default">
  41             <div class="panel panel-heading">
  42                 <h1 class="panel-title">Overview of the Command Line Client</h1>
  43             </div>
  44             <div class="panel-body">
  45                 <p class="justify">
  46                     The command line client comes as a part of
  47                     <a href="${pageContext.request.contextPath}/download.jsp#client">client package</a>
  48                     which you are welcome to download.
  49                     The command line client can be used to align sequences using any of JABAWS supported web
  50                     services. The client is OS independent and supports most of
  51                     the functions which can be accessed programmatically via
  52                     <a href="${pageContext.request.contextPath}/full_javadoc/">JABAWS API</a>. Using this client you could align sequences
  53                     using presets or custom parameters, please see examples of this below. Here is the
  54                     list of options supported by the command line client.
  55                 </p>
  56             </div>
  57         </div>
  58     </div>
  59 </div>
  60 <div class="row" id="usingcclient2">
  61     <div class="col-md-12">
  62         <div class="panel panel-default">
  63             <div class="panel panel-heading">
  64                 <h1 class="panel-title">Command Line Client Usage</h1>
  65             </div>
  66             <div class="panel-body">
  67                 <pre><code class="bash">java -jar jaba-client.jar</code></pre>
  68                 <pre><strong>Usage:</strong>
  69 java -jar &lt;path_to_jar_file&gt; -h=host_and_context -s=serviceName ACTION [OPTIONS]
  70 -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
  71 -s=&lt;ServiceName&gt; - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
  72 <br/>
  73 <strong>ACTIONS:</strong>
  74 -i=&lt;inputFile&gt; - full path to fasta formatted sequence file, from which to align sequences
  75 -parameters - lists parameters supported by web service
  76 -presets - lists presets supported by web service
  77 -limits - lists web services limits
  78 Please note that if input file is specified other actions are ignored
  79 <br/>
  80 <strong> OPTIONS:</strong> (only for use with -i action):
  81 -r=&lt;presetName&gt; - name of the preset to use
  82 -o=&lt;outputFile&gt; - full path to the file where to write an alignment
  83 -f=&lt;parameterInputFile&gt; - the name of the file with the list of parameters to use.<br />
  84 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>
  85             </div>
  86         </div>
  87     </div>
  88 </div>
  89 <div class="row" id="usingcclient3">
  90     <div class="col-md-12">
  91         <div class="panel panel-default">
  92             <div class="panel panel-heading">
  93                 <h1 class="panel-title">Example Usage</h1>
  94             </div>
  95             <div class="panel-body">
  96                 <p class="justify">
  97                     Align sequences from input.fasta file using Mafft web
  98                     service with default settings, print alignment in Clustal format to console.
  99                 </p>
 100                 <pre><code class="bash">java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta</code></pre>
 101                 <p class="justify">
 102                     Content of input.fasta file is show below (please note sequences has been
 103                     trimmed for clarity)
 104                 </p>
 105                 <pre>&gt;Foobar
 106 MTADGPRELLQLRAAVRHRPQDFVAWL
 107 &gt;Bar
 108 MGDTTAGEMAVQRGLALHQ
 109 &gt;Foofriend
 110 MTADGPRELLQLRAAV</pre>
 111                 <p class="justify">
 112                     Align as in above example, but write output alignment in a
 113                     file out.clustal, using parameters defined in prm.in file
 114                 </p>
 115                 <pre><code class="bash">java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws  -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in</code></pre>
 116                 <p class="justify">
 117                     The content of the prm.in file is shown below
 118                 <pre><code class="bash">--nofft
 119 --noscore
 120 --fastaparttree
 121 --retree=10
 122 --op=2.2</code></pre>
 123                 <p class="justify">
 124                     The format of the file is the same for all JABAWS web services.
 125                     Parameters are specified in exactly the same way as for native
 126                     executables - alignment programs like Mafft etc. So parameters
 127                     which you can use with command line version of an alignment program
 128                     can be used with JABAWS. Most of the settings controlling alignment
 129                     process are supported, but because any output has to be handled by
 130                     JABAWS, settings controlling output are not allowed to be changed.
 131                     For a list of parameters supported by a web service see the next example.
 132                     In <em2>prm.in</em2> parameters are separated by the new line, and
 133                     name of the parameter is separated from its value with an equals
 134                     sign. This format is constant no matter which JABAWS web service is used.
 135                 </p>
 136                 <pre><code class="bash">java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters</code></pre>
 137
 138                 <p class="justify">
 139                     The same client can be used to access JABAWS on different hosts.
 140                     Just point the client to the host you want to use by changing the
 141                     value of -h key.
 142                 </p>
 143                 <p class="justify">
 144                     For example you used
 145                     <em2>-h=http://myhost.compbio.ac.uk:8080/jabaws</em2> server,
 146                     now you want to use another server to
 147                     <em2>-h=http://mylabserver.myuni.edu.</em2> This comes handy if
 148                     your favorite server is off and you need to do the job yesterday.
 149                 </p>
 150             </div>
 151         </div>
 152     </div>
 153 </div>
 154
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