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11 <c:param name="title">Documentation</c:param>
14 <ol class="breadcrumb">
15 <li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
16 <li><a href="man_docs.jsp">Documentation</a></li>
17 <li class="active"><a href="man_server_dev.jsp">Develop JABAWS</a></li>
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21 <div class="panel panel-default">
22 <div class="panel panel-heading">
23 <h1 class="panel-title">Command Line Client</h1>
25 <div class="panel-body">
28 <li><a href="#usingcclient1">Overview of the Command Line Client</a></li>
29 <li><a href="#usingcclient2">Command Line Client Usage</a></li>
30 <li><a href="#usingcclient3">Example Usage</a></li>
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38 <div class="row" id="usingcclient1">
39 <div class="col-md-12">
40 <div class="panel panel-default">
41 <div class="panel panel-heading">
42 <h1 class="panel-title">Overview of the Command Line Client</h1>
44 <div class="panel-body">
46 The command line client comes as a part of
47 <a href="${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.
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63 <div class="panel panel-heading">
64 <h1 class="panel-title">Command Line Client Usage</h1>
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 <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
70 -h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
71 -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
73 <strong>ACTIONS:</strong>
74 -i=<inputFile> - 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
80 <strong> OPTIONS:</strong> (only for use with -i action):
81 -r=<presetName> - name of the preset to use
82 -o=<outputFile> - full path to the file where to write an alignment
83 -f=<parameterInputFile> - 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>
89 <div class="row" id="usingcclient3">
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91 <div class="panel panel-default">
92 <div class="panel panel-heading">
93 <h1 class="panel-title">Example Usage</h1>
95 <div class="panel-body">
97 Align sequences from input.fasta file using Mafft web
98 service with default settings, print alignment in Clustal format to console.
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>
102 Content of input.fasta file is show below (please note sequences has been
106 MTADGPRELLQLRAAVRHRPQDFVAWL
110 MTADGPRELLQLRAAV</pre>
112 Align as in above example, but write output alignment in a
113 file out.clustal, using parameters defined in prm.in file
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>
117 The content of the prm.in file is shown below
118 <pre><code class="bash">--nofft
122 --op=2.2</code></pre>
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.
136 <pre><code class="bash">java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters</code></pre>
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
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.
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