Changeset 2554


Ignore:
Timestamp:
Aug 5, 2014, 11:19:33 AM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #614: Improve error handling when executing jobs on the cluster

Added call to picard MarkDuplicates. It is using the unmodifed picard version since the script has not set the PicardDir option. This option is currently specified in the <demux> section. I think we should re-arrange some configuration options so that they can be re-used in different places.

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MaskAlignServlet.java

    r2553 r2554  
    369369          script.cmd("mkdir -p " + tmpFolder);
    370370          script.cmd("cd " + tmpFolder);
     371          script.cmd("cp ${ScriptDir}/stdwrap.sh .");
    371372          script.cmd("cp ${ScriptDir}/picard .");
    372373          script.cmd("cp ${ScriptDir}/statistics_tophat.sh .");
     
    421422          script.cmd(tophatCmd);
    422423          script.newLine();
    423          
     424
     425          script.progress(60, "Running picard MarkDuplicates");
     426          String picardCmd = "./picard MarkDuplicates";
     427          picardCmd += " INPUT=fastq.masked.tophat/accepted_hits.bam";
     428          picardCmd += " OUTPUT=fastq.masked.tophat/accepted_hits.bam.tmp_picard";
     429          picardCmd += " METRICS_FILE=fastq.masked.tophat/accepted_hits_picardmetrics.csv";
     430          picardCmd += " REMOVE_DUPLICATES=false";
     431          picardCmd += " ASSUME_SORTED=true";
     432          picardCmd += " > " + jobFolder + "/picard_MarkDuplicates.out";
     433          script.cmd(picardCmd);
     434          script.cmd("mv fastq.masked.tophat/accepted_hits.bam.tmp_picard fastq.masked.tophat/accepted_hits.bam");
     435
    424436          // TODO - other scripts from tophat_single.sh script
    425437
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