Changeset 5475


Ignore:
Timestamp:
Jun 5, 2019, 4:21:22 PM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1142: Create MIPs flow cell and start sequencing

The "Auto-analyze" option should now work for HiSeq. It has not been tested fully. If it works it will most likely try to start a RNAseq demux so it will probably fail soon after that.

Location:
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie
Files:
1 added
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/NextSeqSignalHandler.java

    r4306 r5475  
    205205            numLanes = Values.getInt(value);
    206206          }
    207           else if ("Read1".equals(key) || "Read2".equals(key) || "Index1Read".equals(key))
     207          else if ("Read1".equals(key) || "Read2".equals(key) || "Index1Read".equals(key) || "Index2Read".equals(key))
    208208          {
    209209            numReads += Values.getInt(value);
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/ReggieSignalHandlerFactory.java

    r4889 r5475  
    7878      handlers = new SignalHandler[] { new NextSeqSignalHandler(job) };
    7979    }
     80    else if ("HiSeq".equals(signalType))
     81    {
     82      handlers = new SignalHandler[] { new HiSeqSignalHandler(job) };
     83    }
    8084   
    8185    return handlers;
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

    r5473 r5475  
    6262import net.sf.basedb.reggie.dao.SequencingRun;
    6363import net.sf.basedb.reggie.dao.Subtype;
     64import net.sf.basedb.reggie.extensions.HiSeqSignalHandler;
    6465import net.sf.basedb.reggie.extensions.NextSeqSignalHandler;
    6566import net.sf.basedb.reggie.grid.ScriptUtil;
     
    386387        Annotationtype.CLUSTER_START.setAnnotationValue(dc, flowCell, startDate);
    387388        Annotationtype.FLOWCELL_ID.setAnnotationValue(dc, flowCell, flowCellBarcode);
     389        String flowCellType = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);
    388390       
    389391        // Load pool aliquots for all lanes and set creation date
     
    455457            job.setExternalId(flowCellBarcode);
    456458           
    457             // TODO - Add support for HiSeq
    458             String signalURI = NextSeqSignalHandler.getSignalUri(flowCellBarcode);
     459            String signalURI = "HiSeq".equals(flowCellType) ?
     460              HiSeqSignalHandler.getSignalUri(flowCellBarcode) :
     461              NextSeqSignalHandler.getSignalUri(flowCellBarcode);
    459462            job.setSignalTransporter(ExtensionSignalTransporter.class, signalURI);
    460463           
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