extensions/net.sf.basedb.reggie/trunk/resources/dnaseq-analysis/vcall_start.jsp

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7400 07 Nov 23 nicklas 1 <%@ page
7400 07 Nov 23 nicklas 2   pageEncoding="UTF-8"
7400 07 Nov 23 nicklas 3   session="false"
7400 07 Nov 23 nicklas 4   import="net.sf.basedb.core.User"
7400 07 Nov 23 nicklas 5   import="net.sf.basedb.core.DbControl"
7400 07 Nov 23 nicklas 6   import="net.sf.basedb.core.SessionControl"
7400 07 Nov 23 nicklas 7   import="net.sf.basedb.core.Application"
7400 07 Nov 23 nicklas 8   import="net.sf.basedb.clients.web.Base"  
7400 07 Nov 23 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
7400 07 Nov 23 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
7400 07 Nov 23 nicklas 11 %>
7400 07 Nov 23 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
7400 07 Nov 23 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
7400 07 Nov 23 nicklas 14 <%
7400 07 Nov 23 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
7400 07 Nov 23 nicklas 16 final String ID = sc.getId();
7400 07 Nov 23 nicklas 17 final float scale = Base.getScale(sc);
7400 07 Nov 23 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
7400 07 Nov 23 nicklas 19 DbControl dc = null;
7400 07 Nov 23 nicklas 20 try
7400 07 Nov 23 nicklas 21 {
7400 07 Nov 23 nicklas 22   dc = sc.newDbControl();
7400 07 Nov 23 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
7400 07 Nov 23 nicklas 24 %>
7400 07 Nov 23 nicklas 25 <base:page type="default" >
7400 07 Nov 23 nicklas 26 <base:head 
7400 07 Nov 23 nicklas 27   scripts="~../reggie-2.js,~vcall_start.js" 
7400 07 Nov 23 nicklas 28   styles="path.css,~../css/reggie-2.css"
7400 07 Nov 23 nicklas 29 />
7400 07 Nov 23 nicklas 30 <base:body>
7400 07 Nov 23 nicklas 31
7400 07 Nov 23 nicklas 32   <p:path><p:pathelement 
7400 07 Nov 23 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
7400 07 Nov 23 nicklas 34     /><p:pathelement title="Start WGS variant calling" 
7400 07 Nov 23 nicklas 35     /></p:path>
7400 07 Nov 23 nicklas 36
7400 07 Nov 23 nicklas 37   <div class="content">
7400 07 Nov 23 nicklas 38   <form name="reggie" id="wizard" class="wizard">
7400 07 Nov 23 nicklas 39
7400 07 Nov 23 nicklas 40   <div class="step auto-hide" id="step-1">
7400 07 Nov 23 nicklas 41     <div class="step-no">1</div>
7400 07 Nov 23 nicklas 42     <div class="step-title">Select tumor/normal aligned sequences</div>
7400 07 Nov 23 nicklas 43     <div class="step-content">
7400 07 Nov 23 nicklas 44     
7400 07 Nov 23 nicklas 45       <table class="step-form">
7400 07 Nov 23 nicklas 46       <tr class="align-top">
7400 07 Nov 23 nicklas 47         <td class="prompt">Tumor/normal pairs</td>
7400 07 Nov 23 nicklas 48         <td class="input">
7400 07 Nov 23 nicklas 49           <select class="required yellow-label-support" multiple size="30"
7400 07 Nov 23 nicklas 50             name="alignedSequences" id="alignedSequences"></select>
7400 07 Nov 23 nicklas 51             
7400 07 Nov 23 nicklas 52           <base:buttongroup style="margin-top: 0.5em;">
7400 07 Nov 23 nicklas 53             <base:button title="Select manually&hellip;" id="btnSelectAlignedSequences" />
7400 07 Nov 23 nicklas 54           </base:buttongroup>
7400 07 Nov 23 nicklas 55         </td>
7400 07 Nov 23 nicklas 56         <td class="status" id="alignedSequences.status"></td>
7400 07 Nov 23 nicklas 57         <td class="help"><span id="alignedSequences.message" class="message"></span>
7400 07 Nov 23 nicklas 58           Select the tumor and normal aligned sequences that should be processed. 
7400 07 Nov 23 nicklas 59           The list contains aligned sequences  from the <b>WGS variant calling pipeline</b> 
7400 07 Nov 23 nicklas 60           item list (max 50).<br><br> Items marked with <b>[R]</b> have been marked for re-processing 
7400 07 Nov 23 nicklas 61           due to a  previous failure.
7400 07 Nov 23 nicklas 62         </td>
7400 07 Nov 23 nicklas 63       </tr>
7400 07 Nov 23 nicklas 64       </table>
7400 07 Nov 23 nicklas 65
7400 07 Nov 23 nicklas 66     </div>
7400 07 Nov 23 nicklas 67   </div>
7400 07 Nov 23 nicklas 68   
7400 07 Nov 23 nicklas 69   <div class="step" id="step-2">
7400 07 Nov 23 nicklas 70     <div class="step-no">2</div>
7400 07 Nov 23 nicklas 71     <div class="step-title">Parameters</div>
7400 07 Nov 23 nicklas 72     <div class="step-content">
7400 07 Nov 23 nicklas 73
7400 07 Nov 23 nicklas 74       <table class="step-form">
7400 07 Nov 23 nicklas 75       <tbody>
7400 07 Nov 23 nicklas 76         <tr>
7439 16 Nov 23 nicklas 77           <td class="prompt">Panel-of-normal</td>
7439 16 Nov 23 nicklas 78           <td class="input">
7439 16 Nov 23 nicklas 79             <select name="panelOfNormals" id="panelOfNormals" class="required">
7439 16 Nov 23 nicklas 80               <option value="">- auto -
7439 16 Nov 23 nicklas 81             </select>
7439 16 Nov 23 nicklas 82           </td>
7439 16 Nov 23 nicklas 83           <td class="status" id="panelOfNormals.status"></td>
7439 16 Nov 23 nicklas 84           <td class="help"><span id="panelOfNormals.message" class="message"></span>
7439 16 Nov 23 nicklas 85             Select which panel-of-normals that should be used in the variant calling.
7439 16 Nov 23 nicklas 86             The <b>auto</b> option will select a panel based on the <b>ExternalOperator</b>
7439 16 Nov 23 nicklas 87             annotation (taken from the parent Library item).
7439 16 Nov 23 nicklas 88           </td>
7439 16 Nov 23 nicklas 89         </tr>
7439 16 Nov 23 nicklas 90         <tr>
7400 07 Nov 23 nicklas 91           <td class="prompt">Software</td>
7400 07 Nov 23 nicklas 92           <td class="input">
7400 07 Nov 23 nicklas 93             <select name="vcallSoftware" id="vcallSoftware"></select>
7400 07 Nov 23 nicklas 94           </td>
7400 07 Nov 23 nicklas 95           <td class="status" id="vcallSoftware.status"></td>
7400 07 Nov 23 nicklas 96           <td class="help">
7400 07 Nov 23 nicklas 97             <span id="vcallSoftware.message" class="message"></span>
7400 07 Nov 23 nicklas 98             Select the software to use.
7400 07 Nov 23 nicklas 99           </td>
7400 07 Nov 23 nicklas 100         </tr>
7400 07 Nov 23 nicklas 101       </tbody>
7400 07 Nov 23 nicklas 102       <tbody class="info-section">
7400 07 Nov 23 nicklas 103         <tr>
7400 07 Nov 23 nicklas 104           <td class="subprompt">Parameter set</td>
7400 07 Nov 23 nicklas 105           <td class="info" colspan="2">
7400 07 Nov 23 nicklas 106             <span id="vcallSoftware.parameterSet"></span>
7400 07 Nov 23 nicklas 107             <div id="vcallSoftware.description" class="item-description"></div>
7400 07 Nov 23 nicklas 108           </td>
7400 07 Nov 23 nicklas 109           <td class="help">
7400 07 Nov 23 nicklas 110             This step uses Mutect2 for variant calling. Parameters are configured in 
7400 07 Nov 23 nicklas 111             the &lt;wgs-variant-call&gt; section in reggie-config.xml.
7400 07 Nov 23 nicklas 112           </td>
7400 07 Nov 23 nicklas 113         </tr>
7400 07 Nov 23 nicklas 114       </tbody>
7400 07 Nov 23 nicklas 115       <tbody>
7400 07 Nov 23 nicklas 116         <tr class="section-header">
7400 07 Nov 23 nicklas 117           <td colspan="4">Job scheduler</td>
7400 07 Nov 23 nicklas 118         </tr>
7400 07 Nov 23 nicklas 119         <tr>
7400 07 Nov 23 nicklas 120           <td class="subprompt">Cluster</td>
7400 07 Nov 23 nicklas 121           <td class="input">
7400 07 Nov 23 nicklas 122             <select name="clusters" id="clusters" class="required"></select></td>
7400 07 Nov 23 nicklas 123           <td class="status" id="clusters.status"></td>
7400 07 Nov 23 nicklas 124           <td class="help">
7400 07 Nov 23 nicklas 125             <span id="clusters.message" class="message"></span>
7400 07 Nov 23 nicklas 126             Select the cluster to use for running the software.
7400 07 Nov 23 nicklas 127           </td>
7400 07 Nov 23 nicklas 128         </tr>
7400 07 Nov 23 nicklas 129         <tr id="job-priority" style="display: none;">
7400 07 Nov 23 nicklas 130           <td class="subprompt">Job priority</td>
7400 07 Nov 23 nicklas 131           <td class="input">
7400 07 Nov 23 nicklas 132             <select name="priority" id="priority"></select>
7400 07 Nov 23 nicklas 133           </td>
7400 07 Nov 23 nicklas 134           <td class="status" id="priority.status"></td>
7400 07 Nov 23 nicklas 135           <td class="help">
7400 07 Nov 23 nicklas 136             <span id="priority.message" class="message"></span>
7400 07 Nov 23 nicklas 137             Select the priority of the job.
7400 07 Nov 23 nicklas 138           </td>
7400 07 Nov 23 nicklas 139         </tr>
7400 07 Nov 23 nicklas 140         <tr id="job-partition" style="display: none;">
7400 07 Nov 23 nicklas 141           <td class="subprompt">Job partition</td>
7400 07 Nov 23 nicklas 142           <td class="input">
7400 07 Nov 23 nicklas 143             <select name="partition" id="partition"></select>
7400 07 Nov 23 nicklas 144           </td>
7400 07 Nov 23 nicklas 145           <td class="status" id="partition.status"></td>
7400 07 Nov 23 nicklas 146           <td class="help">
7400 07 Nov 23 nicklas 147             <span id="partition.message" class="message"></span>
7400 07 Nov 23 nicklas 148             Select the partition/queue that the job should be submitted to.
7400 07 Nov 23 nicklas 149           </td>
7400 07 Nov 23 nicklas 150         </tr>
7400 07 Nov 23 nicklas 151       </tbody>
7400 07 Nov 23 nicklas 152       <tbody class="info-section">
7400 07 Nov 23 nicklas 153         <tr class="align-top">
7400 07 Nov 23 nicklas 154           <td class="subprompt">Job options</td>
7400 07 Nov 23 nicklas 155           <td class="info input">
7400 07 Nov 23 nicklas 156             <div id="submitOptions" class="item-description code"></div>
7400 07 Nov 23 nicklas 157             <textarea id="submitOptionsOverride" name="submitOptionsOverride" rows="4" style="display: none;"></textarea>
7400 07 Nov 23 nicklas 158           </td>
7400 07 Nov 23 nicklas 159           <td class="status" id="submitOptions.status">
7400 07 Nov 23 nicklas 160             <input type="checkbox" id="override" name="override" title="Override the default options" disabled>
7400 07 Nov 23 nicklas 161           </td>
7400 07 Nov 23 nicklas 162           <td class="help">
7400 07 Nov 23 nicklas 163             Parameters are configured in the &lt;wgs-variant-call&gt;/&lt;submit&gt; 
7400 07 Nov 23 nicklas 164             section in reggie-config.xml. Select the checkbox to manually 
7400 07 Nov 23 nicklas 165             override the default options.
7400 07 Nov 23 nicklas 166           </td>
7400 07 Nov 23 nicklas 167         </tr>
7400 07 Nov 23 nicklas 168       </tbody>
7400 07 Nov 23 nicklas 169       <tbody>
7400 07 Nov 23 nicklas 170         <tr>
7438 16 Nov 23 nicklas 171           <td class="subprompt">Auto-confirm</td>
7438 16 Nov 23 nicklas 172           <td class="input"><input type="checkbox" name="autoConfirm" id="autoConfirm" checked></td>
7400 07 Nov 23 nicklas 173           <td class="status" id="autoConfirm.status"></td>
7400 07 Nov 23 nicklas 174           <td class="help">
7400 07 Nov 23 nicklas 175             <span id="autoConfirm.message" class="message"></span>
7400 07 Nov 23 nicklas 176             Currently not used since there is no further steps in this part of pipeline.
7400 07 Nov 23 nicklas 177           </td>
7400 07 Nov 23 nicklas 178         </tr>
7400 07 Nov 23 nicklas 179         <tr>
7400 07 Nov 23 nicklas 180           <td class="subprompt">Debug</td>
7400 07 Nov 23 nicklas 181           <td class="input"><input type="checkbox" name="debug" id="debug"></td>
7400 07 Nov 23 nicklas 182           <td class="status" id="debug.status"></td>
7400 07 Nov 23 nicklas 183           <td class="help">
7400 07 Nov 23 nicklas 184             <span id="debug.message" class="message"></span>
7400 07 Nov 23 nicklas 185             When running in debug mode temporary files are not removed from the
7400 07 Nov 23 nicklas 186             cluster node.
7400 07 Nov 23 nicklas 187           </td>
7400 07 Nov 23 nicklas 188         </tr>
7400 07 Nov 23 nicklas 189       </tbody>
7400 07 Nov 23 nicklas 190       </table>
7400 07 Nov 23 nicklas 191     </div>
7400 07 Nov 23 nicklas 192   </div>
7400 07 Nov 23 nicklas 193     
7400 07 Nov 23 nicklas 194     <div id="wizard-status"></div>
7400 07 Nov 23 nicklas 195   
7400 07 Nov 23 nicklas 196     <table class="navigation" id="navigation">
7400 07 Nov 23 nicklas 197     <tr>
7400 07 Nov 23 nicklas 198       <td><base:button id="gocancel" title="Cancel" /></td>
7400 07 Nov 23 nicklas 199       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
7400 07 Nov 23 nicklas 200       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
7400 07 Nov 23 nicklas 201       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
7400 07 Nov 23 nicklas 202       <td id="gonext-message" class="message"></td>
7400 07 Nov 23 nicklas 203     </tr>
7400 07 Nov 23 nicklas 204     </table>
7400 07 Nov 23 nicklas 205   
7400 07 Nov 23 nicklas 206   </form>
7400 07 Nov 23 nicklas 207   </div>
7400 07 Nov 23 nicklas 208   
7400 07 Nov 23 nicklas 209 </base:body>
7400 07 Nov 23 nicklas 210 </base:page>
7400 07 Nov 23 nicklas 211 <%
7400 07 Nov 23 nicklas 212 }
7400 07 Nov 23 nicklas 213 finally
7400 07 Nov 23 nicklas 214 {
7400 07 Nov 23 nicklas 215   if (dc != null) dc.close();
7400 07 Nov 23 nicklas 216 }
7400 07 Nov 23 nicklas 217 %>

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