website/man_docs.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 class="active"><a href="man_docs.jsp">Documentation</a></li>
  17 </ol>
  18 <div class="row">
  19     <div class="col-md-12">
  20         <div class="panel panel-default">
  21             <div class="panel panel-heading">
  22                 <h1 class="panel-title">JABAWS Documentation</h1>
  23             </div>
  24             <div class="panel-body">
  25                 <ul>
  26                     <li>
  27                         <a href="man_about.jsp">What is JABAWS?</a>
  28                         <ul>
  29                             <li><a href="man_about.jsp#wisjaba">What is JABAWS?</a></li>
  30                             <li><a href="man_about.jsp#wjaba">JABAWS Benefits</a></li>
  31                             <li><a href="man_about.jsp#alprog">JABA Web Services Programs</a></li>
  32                             <li><a href="man_about.jsp#jaba2.2">What is new in JABAWS 2.2?</a> </li>
  33                             <li><a href="man_about.jsp#jabaclient">What is JABAWS Client</a>?</li>
  34                             <li><a href="man_about.jsp#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
  35                             <li><a href="man_about.jsp#cmdclient">Programmatic access to JABAWS</a></li>
  36                         </ul>
  37                     </li>
  38                     <br/>
  39                     <li>
  40                         <a href="man_servervm.jsp">Virtual Appliance</a>
  41                         <ul>
  42                             <li><a href="man_servervm.jsp#whatisvm">What is JABAWS Virtual Appliance?</a></li>
  43                             <li><a href="man_servervm.jsp#whenvm">When to use the Virtual Appliance</a> </li>
  44                             <li><a href="man_servervm.jsp#howtoinstallvm">How to install VMware Player </a></li>
  45                             <li><a href="man_servervm.jsp#vmplayer">VMware Player Appliance configuration </a></li>
  46                             <li><a href="man_servervm.jsp#jabawsAppliance">JABAWS Appliance details </a></li>
  47                             <li><a href="man_servervm.jsp#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>
  48                             <li><a href="man_servervm.jsp#vmiaccess">VM Network Settings </a></li>
  49                         </ul>
  50                     </li>
  51                     <br/>
  52                     <li>
  53                         <a href="man_serverwar.jsp">Web Application Archive</a>
  54                         <ul>
  55                             <li><a href="man_serverwar.jsp#sysreq">System Requirements</a></li>
  56                             <li><a href="man_serverwar.jsp#instwar">Installing the JABAWS WAR file</a></li>
  57                             <li><a href="man_serverwar.jsp#prepexec">Preparing executables for use with JABAWS</a></li>
  58                             <li><a href="man_serverwar.jsp#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>
  59                             <li><a href="man_serverwar.jsp#recompbinaries">Recompiling the bundled programs for your system</a></li>
  60                             <li><a href="man_serverwar.jsp#haveexec">Reuse the binaries that are already in your system</a></li>
  61                             <li><a href="man_serverwar.jsp#obtainexec">Obtaining command line binaries </a><a href="#obtainexec">for your operating system</a></li>
  62                             <li><a href="man_serverwar.jsp#usingWsTester">Testing JABAWS Server</a></li>
  63                             <li><a href="man_serverwar.jsp#diffcontexts">Running many JABAWS instances on the same server</a> </li>
  64                             <li><a href="man_serverwar.jsp#nocluster">JABAWS on a single server</a></li>
  65                             <li><a href="man_serverwar.jsp#clustsubsys">JABAWS supported cluster batch management systems </a></li>
  66                             <li><a href="man_serverwar.jsp#tomstopundeploy">Manually deploying JABAWS application on Apache-Tomcat </a></li>
  67                             <li><a href="man_serverwar.jsp#tomdeploy">Apache-Tomcat fails to deploy the jabaws.war file</a></li>
  68                         </ul>
  69                     </li>
  70                     <br/>
  71                     <li>
  72                         <a href="man_client.jsp">Command Line Client</a>
  73                     </li>
  74                     <br/>
  75                     <li>
  76                         <a href="man_configuration.jsp">Configure JABAWS</a>
  77                         <ul>
  78                             <li><a href="man_configuration.jsp#defjabaconf">JABAWS Configuration </a></li>
  79                             <li><a href="man_configuration.jsp#locEngConf">Local Engine Configuration</a></li>
  80                             <li><a href="man_configuration.jsp#clustEngConf">Cluster Engine Configuration</a></li>
  81                             <li><a href="man_configuration.jsp#exec">Executable Configuration</a></li>
  82                             <li><a href="man_configuration.jsp#setexecenv">Defining Environment Variables for Executables</a></li>
  83                             <li><a href="man_configuration.jsp#mafftconf">Configure JABAWS to Work with Mafft</a></li>
  84                             <li><a href="man_configuration.jsp#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>
  85                             <li><a href="man_configuration.jsp#diffbin">Using a different version of the alignment program with JABAWS</a></li>
  86                             <li><a href="man_configuration.jsp#mixuse">Load balancing </a></li>
  87                             <li><a href="man_configuration.jsp#testingJaba">Testing JABA Web Services</a></li>
  88                             <li><a href="man_configuration.jsp#logs">JABAWS requests logging </a></li>
  89                             <li><a href="man_configuration.jsp#logfiles">JABAWS internal logging </a></li>
  90                             <li><a href="man_configuration.jsp#warfile">JABAWS War File Content</a></li>
  91                             <li><a href="man_configuration.jsp#ga">JABAWS and Google Analytics</a></li>
  92                         </ul>
  93                     </li>
  94                     <br/>
  95                     <li>
  96                         <a href="man_dev.jsp">Accessing JABAWS</a>
  97                         <ul>
  98                             <li><a href="man_dev.jsp#wsfunctions">Web services functions overview </a></li>
  99                             <li><a href="man_dev.jsp#templatestr">The template client structure</a></li>
 100                             <li><a href="man_dev.jsp#connectto">Connecting to JABAWS</a></li>
 101                             <li><a href="man_dev.jsp#validnames">Valid JABAWS service names and WSDL files</a></li>
 102                             <li><a href="man_dev.jsp#defalign">Aligning sequences</a></li>
 103                             <li><a href="man_dev.jsp#checkresults">Checking the status of the calculation </a></li>
 104                             <li><a href="man_dev.jsp#presetalign">Aligning with presets</a></li>
 105                             <li><a href="man_dev.jsp#customalign">Aligning with custom parameters</a></li>
 106                             <li><a href="man_dev.jsp#writingaltofile">Writing alignments to a file</a></li>
 107                             <li><a href="man_dev.jsp#compex">A complete client example </a></li>
 108                             <li><a href="man_dev.jsp#buildart">Building web services artifacts</a></li>
 109                         </ul>
 110                     </li>
 111                     <br/>
 112                     <li>
 113                         <a href="man_server_dev.jsp">Develop JABAWS</a>
 114                         <ul>
 115                             <li><a href="man_server_dev.jsp#api">The API</a></li>
 116                             <li><a href="man_server_dev.jsp#thesrc">The source code</a></li>
 117                             <li><a href="man_server_dev.jsp#projstruct">Structure of the project</a></li>
 118                             <li><a href="man_server_dev.jsp#thecode">The code structure</a></li>
 119                             <li><a href="man_server_dev.jsp#runtests">Running tests</a></li>
 120                             <li><a href="man_server_dev.jsp#prepexec">Preparing distributive's</a></li>
 121                             <li><a href="man_server_dev.jsp#buildstubs">Building web services artifacts</a></li>
 122                             <li><a href="man_server_dev.jsp#addnewws">Adding a new web service (rough guide)</a></li>
 123                         </ul>
 124                     </li>
 125                     <br/>
 126                     <li>
 127                         <a href="man_stats.jsp">Usage Statistics</a>
 128                         <ul>
 129                             <li><a href="man_stats.jsp#usage_sum">Summary of Usage</a></li>
 130                             <li><a href="man_stats.jsp#helpUsageStats">Authentication</a></li>
 131                             <li><a href="man_stats.jsp#detailed_usage">Detailed Usage Statistic </a></li>
 132                             <li><a href="man_stats.jsp#job_list">Job List</a></li>
 133                             <li><a href="man_stats.jsp#job_dir">Single Job Directory Content </a></li>
 134                             <li><a href="man_stats.jsp#conf_tomcat_user">Configuring a privileged   access for Tomcat web application server</a></li>
 135                             <li><a href="man_stats.jsp#exec_stat_conf">Configuring JABAWS execution statistics</a></li>
 136                         </ul>
 137                     </li>
 138                     <br/>
 139                 </ul>
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 144     </div>
 145 </div>
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