extensions/net.sf.basedb.reggie/trunk/resources/analysis/stringtie_start.jsp

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4661 29 Jan 18 nicklas 1 <%@ page
4661 29 Jan 18 nicklas 2   pageEncoding="UTF-8"
4661 29 Jan 18 nicklas 3   session="false"
4661 29 Jan 18 nicklas 4   import="net.sf.basedb.core.User"
4661 29 Jan 18 nicklas 5   import="net.sf.basedb.core.DbControl"
4661 29 Jan 18 nicklas 6   import="net.sf.basedb.core.SessionControl"
4661 29 Jan 18 nicklas 7   import="net.sf.basedb.core.Application"
4661 29 Jan 18 nicklas 8   import="net.sf.basedb.clients.web.Base"  
4661 29 Jan 18 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
4661 29 Jan 18 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
4661 29 Jan 18 nicklas 11 %>
4661 29 Jan 18 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
4661 29 Jan 18 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
4661 29 Jan 18 nicklas 14 <%
4661 29 Jan 18 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
4661 29 Jan 18 nicklas 16 final String ID = sc.getId();
4661 29 Jan 18 nicklas 17 final float scale = Base.getScale(sc);
4661 29 Jan 18 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
4661 29 Jan 18 nicklas 19 DbControl dc = null;
4661 29 Jan 18 nicklas 20 try
4661 29 Jan 18 nicklas 21 {
4661 29 Jan 18 nicklas 22   dc = sc.newDbControl();
4661 29 Jan 18 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
4661 29 Jan 18 nicklas 24 %>
4661 29 Jan 18 nicklas 25 <base:page type="default" >
4661 29 Jan 18 nicklas 26 <base:head 
4661 29 Jan 18 nicklas 27   scripts="~../reggie-2.js,~stringtie_start.js" 
4661 29 Jan 18 nicklas 28   styles="path.css,~../css/reggie-2.css"
4661 29 Jan 18 nicklas 29 />
4661 29 Jan 18 nicklas 30 <base:body>
4661 29 Jan 18 nicklas 31
4661 29 Jan 18 nicklas 32   <p:path><p:pathelement 
4661 29 Jan 18 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
4663 29 Jan 18 nicklas 34     /><p:pathelement title="Start StringTie analysis" 
4661 29 Jan 18 nicklas 35     /></p:path>
4661 29 Jan 18 nicklas 36
4661 29 Jan 18 nicklas 37   <div class="content">
4661 29 Jan 18 nicklas 38   <form name="reggie" id="wizard" class="wizard">
4661 29 Jan 18 nicklas 39
4661 29 Jan 18 nicklas 40   <div class="step auto-hide" id="step-1">
4661 29 Jan 18 nicklas 41     <div class="step-no">1</div>
4661 29 Jan 18 nicklas 42     <div class="step-title">Select aligned sequences</div>
4661 29 Jan 18 nicklas 43     <div class="step-content">
4661 29 Jan 18 nicklas 44     
4661 29 Jan 18 nicklas 45       <table class="step-form">
4661 29 Jan 18 nicklas 46       <tr class="align-top">
4661 29 Jan 18 nicklas 47         <td class="prompt">Aligned sequences</td>
4661 29 Jan 18 nicklas 48         <td class="input">
4661 29 Jan 18 nicklas 49           <select class="required yellow-label-support" multiple size="30"
4661 29 Jan 18 nicklas 50             name="alignedSequences" id="alignedSequences"></select>
4661 29 Jan 18 nicklas 51             
4661 29 Jan 18 nicklas 52           <base:buttongroup style="margin-top: 0.5em;">
4661 29 Jan 18 nicklas 53             <base:button title="Select manually&hellip;" id="btnSelectAlignedSequences" />
4661 29 Jan 18 nicklas 54           </base:buttongroup>
4661 29 Jan 18 nicklas 55         </td>
4661 29 Jan 18 nicklas 56         <td class="status" id="alignedSequences.status"></td>
4661 29 Jan 18 nicklas 57         <td class="help"><span id="alignedSequences.message" class="message"></span>
4663 29 Jan 18 nicklas 58           Select the aligned sequences that should be processed with StringTie. 
4663 29 Jan 18 nicklas 59           The list contains aligned sequences  from the <b>StringTie pipeline</b> item list 
4661 29 Jan 18 nicklas 60           (max 250).<br><br> Items marked with <b>[R]</b> have been marked for re-processing 
4661 29 Jan 18 nicklas 61           due to a  previous failure.
4661 29 Jan 18 nicklas 62         </td>
4661 29 Jan 18 nicklas 63       </tr>
4661 29 Jan 18 nicklas 64       </table>
4661 29 Jan 18 nicklas 65
4661 29 Jan 18 nicklas 66     </div>
4661 29 Jan 18 nicklas 67   </div>
4661 29 Jan 18 nicklas 68   
4661 29 Jan 18 nicklas 69   
4661 29 Jan 18 nicklas 70   <div class="step" id="step-2">
4661 29 Jan 18 nicklas 71     <div class="step-no">2</div>
4663 29 Jan 18 nicklas 72     <div class="step-title">StringTie information</div>
4661 29 Jan 18 nicklas 73     <div class="step-content">
4661 29 Jan 18 nicklas 74
4661 29 Jan 18 nicklas 75       <table class="step-form">
4661 29 Jan 18 nicklas 76       <tbody>
4661 29 Jan 18 nicklas 77         <tr>
4661 29 Jan 18 nicklas 78           <td class="prompt">Array design</td>
4661 29 Jan 18 nicklas 79           <td class="input">
4661 29 Jan 18 nicklas 80             <select name="arrayDesign" id="arrayDesign" class="required"></select>
4661 29 Jan 18 nicklas 81           </td>
4661 29 Jan 18 nicklas 82           <td class="status" id="arrayDesign.status"></td>
4661 29 Jan 18 nicklas 83           <td class="help">
4661 29 Jan 18 nicklas 84             <span id="arrayDesign.message" class="message"></span>
4661 29 Jan 18 nicklas 85             Select the array design to link the data to.
4661 29 Jan 18 nicklas 86           </td>
4661 29 Jan 18 nicklas 87         </tr>
4661 29 Jan 18 nicklas 88         <tr>
4661 29 Jan 18 nicklas 89           <td class="prompt">Protocol</td>
4661 29 Jan 18 nicklas 90           <td class="input">
4661 29 Jan 18 nicklas 91             <select name="stringtieProtocol" id="stringtieProtocol"></select>
4661 29 Jan 18 nicklas 92           </td>
4661 29 Jan 18 nicklas 93           <td class="status" id="stringtieProtocol.status"></td>
4661 29 Jan 18 nicklas 94           <td class="help">
4661 29 Jan 18 nicklas 95             <span id="stringtieProtocol.message" class="message"></span>
4661 29 Jan 18 nicklas 96             Select the protocol used.
4661 29 Jan 18 nicklas 97           </td>
4661 29 Jan 18 nicklas 98         </tr>
4661 29 Jan 18 nicklas 99         <tr>
4661 29 Jan 18 nicklas 100           <td class="prompt">Software</td>
4661 29 Jan 18 nicklas 101           <td class="input">
4661 29 Jan 18 nicklas 102             <select name="stringtieSoftware" id="stringtieSoftware"></select>
4661 29 Jan 18 nicklas 103           </td>
4661 29 Jan 18 nicklas 104           <td class="status" id="stringtieSoftware.status"></td>
4661 29 Jan 18 nicklas 105           <td class="help">
4661 29 Jan 18 nicklas 106             <span id="stringtieSoftware.message" class="message"></span>
4661 29 Jan 18 nicklas 107             Select the software to use.
4661 29 Jan 18 nicklas 108           </td>
4661 29 Jan 18 nicklas 109         </tr>
4661 29 Jan 18 nicklas 110       </tbody>
4661 29 Jan 18 nicklas 111       <tbody class="info-section">
4661 29 Jan 18 nicklas 112         <tr>
4661 29 Jan 18 nicklas 113           <td class="subprompt">Parameter set</td>
4661 29 Jan 18 nicklas 114           <td class="info" colspan="2">
4661 29 Jan 18 nicklas 115             <span id="stringtieSoftware.parameterSet"></span>
4661 29 Jan 18 nicklas 116             <div id="stringtieSoftware.description" class="item-description"></div>
4661 29 Jan 18 nicklas 117           </td>
4661 29 Jan 18 nicklas 118           <td class="help">
4663 29 Jan 18 nicklas 119             This step uses StringTie for calculating expression values. Parameters are configured in 
4661 29 Jan 18 nicklas 120             the &lt;stringtie&gt; section in reggie-config.xml.
4661 29 Jan 18 nicklas 121           </td>
4661 29 Jan 18 nicklas 122         </tr>
4661 29 Jan 18 nicklas 123       </tbody>
4661 29 Jan 18 nicklas 124       <tbody>
4661 29 Jan 18 nicklas 125         <tr class="section-header">
6735 09 May 22 nicklas 126           <td colspan="4">Job scheduler</td>
4661 29 Jan 18 nicklas 127         </tr>
4661 29 Jan 18 nicklas 128         <tr>
4661 29 Jan 18 nicklas 129           <td class="subprompt">Cluster</td>
4661 29 Jan 18 nicklas 130           <td class="input">
4661 29 Jan 18 nicklas 131             <select name="clusters" id="clusters" class="required"></select></td>
4661 29 Jan 18 nicklas 132           <td class="status" id="clusters.status"></td>
4661 29 Jan 18 nicklas 133           <td class="help">
4661 29 Jan 18 nicklas 134             <span id="clusters.message" class="message"></span>
4661 29 Jan 18 nicklas 135             Select the cluster to use for running the software.
4661 29 Jan 18 nicklas 136           </td>
4661 29 Jan 18 nicklas 137         </tr>
4661 29 Jan 18 nicklas 138         <tr id="job-priority" style="display: none;">
4661 29 Jan 18 nicklas 139           <td class="subprompt">Job priority</td>
4661 29 Jan 18 nicklas 140           <td class="input">
4661 29 Jan 18 nicklas 141             <select name="priority" id="priority"></select>
4661 29 Jan 18 nicklas 142           </td>
4661 29 Jan 18 nicklas 143           <td class="status" id="priority.status"></td>
4661 29 Jan 18 nicklas 144           <td class="help">
4661 29 Jan 18 nicklas 145             <span id="priority.message" class="message"></span>
4661 29 Jan 18 nicklas 146             Select the priority of the job.
4661 29 Jan 18 nicklas 147           </td>
4661 29 Jan 18 nicklas 148         </tr>
6980 17 Jan 23 nicklas 149         <tr id="job-partition" style="display: none;">
6980 17 Jan 23 nicklas 150           <td class="subprompt">Job partition</td>
6980 17 Jan 23 nicklas 151           <td class="input">
6980 17 Jan 23 nicklas 152             <select name="partition" id="partition"></select>
6980 17 Jan 23 nicklas 153           </td>
6980 17 Jan 23 nicklas 154           <td class="status" id="partition.status"></td>
6980 17 Jan 23 nicklas 155           <td class="help">
6980 17 Jan 23 nicklas 156             <span id="partition.message" class="message"></span>
6980 17 Jan 23 nicklas 157             Select the partition/queue that the job should be submitted to.
6980 17 Jan 23 nicklas 158           </td>
6980 17 Jan 23 nicklas 159         </tr>
7372 06 Oct 23 nicklas 160       </tbody>
7372 06 Oct 23 nicklas 161       <tbody class="info-section">
7372 06 Oct 23 nicklas 162         <tr class="align-top">
7372 06 Oct 23 nicklas 163           <td class="subprompt">Job options</td>
7372 06 Oct 23 nicklas 164           <td class="info input">
7372 06 Oct 23 nicklas 165             <div id="submitOptions" class="item-description code"></div>
7372 06 Oct 23 nicklas 166             <textarea id="submitOptionsOverride" name="submitOptionsOverride" rows="4" style="display: none;"></textarea>
7372 06 Oct 23 nicklas 167           </td>
7372 06 Oct 23 nicklas 168           <td class="status" id="submitOptions.status">
7372 06 Oct 23 nicklas 169             <input type="checkbox" id="override" name="override" title="Override the default options" disabled>
7372 06 Oct 23 nicklas 170           </td>
7372 06 Oct 23 nicklas 171           <td class="help">
7372 06 Oct 23 nicklas 172             Parameters are configured in the &lt;stringtie&gt;/&lt;submit&gt; 
7372 06 Oct 23 nicklas 173             section in reggie-config.xml. Select the checkbox to manually 
7372 06 Oct 23 nicklas 174             override the default options.
7372 06 Oct 23 nicklas 175           </td>
7372 06 Oct 23 nicklas 176         </tr>
7372 06 Oct 23 nicklas 177       </tbody>
7372 06 Oct 23 nicklas 178       <tbody>
4661 29 Jan 18 nicklas 179         <tr>
4661 29 Jan 18 nicklas 180           <td class="subprompt">Auto-confirm</td>
4661 29 Jan 18 nicklas 181           <td class="input"><input type="checkbox" name="autoConfirm" checked></td>
4661 29 Jan 18 nicklas 182           <td class="status" id="autoConfirm.status"></td>
4661 29 Jan 18 nicklas 183           <td class="help">
4661 29 Jan 18 nicklas 184             <span id="autoConfirm.message" class="message"></span>
6025 26 Oct 20 nicklas 185             If checked, the pipeline will automatically continue with SSP analysis 
6025 26 Oct 20 nicklas 186             and SCAN-B report creation.
4661 29 Jan 18 nicklas 187           </td>
4661 29 Jan 18 nicklas 188         </tr>
4661 29 Jan 18 nicklas 189         <tr>
4661 29 Jan 18 nicklas 190           <td class="subprompt">Debug</td>
7372 06 Oct 23 nicklas 191           <td class="input"><input type="checkbox" name="debug" id="debug"></td>
4661 29 Jan 18 nicklas 192           <td class="status" id="debug.status"></td>
4661 29 Jan 18 nicklas 193           <td class="help">
4661 29 Jan 18 nicklas 194             <span id="debug.message" class="message"></span>
4661 29 Jan 18 nicklas 195             When running in debug mode temporary files are not removed from the
4661 29 Jan 18 nicklas 196             cluster node.
4661 29 Jan 18 nicklas 197           </td>
4661 29 Jan 18 nicklas 198         </tr>
4661 29 Jan 18 nicklas 199       </tbody>
4661 29 Jan 18 nicklas 200       </table>
4661 29 Jan 18 nicklas 201     </div>
4661 29 Jan 18 nicklas 202   </div>
4661 29 Jan 18 nicklas 203     
4661 29 Jan 18 nicklas 204     <div id="wizard-status"></div>
4661 29 Jan 18 nicklas 205   
4661 29 Jan 18 nicklas 206     <table class="navigation" id="navigation">
4661 29 Jan 18 nicklas 207     <tr>
4661 29 Jan 18 nicklas 208       <td><base:button id="gocancel" title="Cancel" /></td>
4661 29 Jan 18 nicklas 209       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
4661 29 Jan 18 nicklas 210       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
4661 29 Jan 18 nicklas 211       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
4661 29 Jan 18 nicklas 212       <td id="gonext-message" class="message"></td>
4661 29 Jan 18 nicklas 213     </tr>
4661 29 Jan 18 nicklas 214     </table>
4661 29 Jan 18 nicklas 215   
4661 29 Jan 18 nicklas 216   </form>
4661 29 Jan 18 nicklas 217   </div>
4661 29 Jan 18 nicklas 218   
4661 29 Jan 18 nicklas 219 </base:body>
4661 29 Jan 18 nicklas 220 </base:page>
4661 29 Jan 18 nicklas 221 <%
4661 29 Jan 18 nicklas 222 }
4661 29 Jan 18 nicklas 223 finally
4661 29 Jan 18 nicklas 224 {
4661 29 Jan 18 nicklas 225   if (dc != null) dc.close();
4661 29 Jan 18 nicklas 226 }
4661 29 Jan 18 nicklas 227 %>

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