Ejemplo n.º 1
0
  private void addCommands() throws IOException {

    String baseName = FilenameUtils.getBaseName(bam.getAbsolutePath());
    File logFile = new File(bam.getParentFile(), baseName + "_qualimap.log");
    File tmpDir = new File("/tmp", baseName);
    File localQualimapReport = new File(tmpDir, "report.pdf");

    String appendAlloutputToLog = " >> " + logFile.getAbsolutePath() + " 2>&1";

    // create a tmp dir
    addCommand("mkdir " + tmpDir + appendAlloutputToLog);
    addCommand("\n");

    addCommand(
        "unset DISPLAY"); // somehow needed to prevent missing X11 error from qualimap when the
                          // pipeline is executed from a user not logged in with - X

    // call the raw variants
    addCommand(
        gc.getQualiMap().getAbsolutePath()
            + " bamqc "
            + " -bam "
            + bam.getAbsolutePath()
            + " -outdir "
            + tmpDir.getAbsolutePath()
            + " -outformat PDF"
            + " -nt "
            + gc.getQualimapSGEThreads()
            + " --java-mem-size="
            + gc.getQualimapSGEMemory()
            + "G"
            + appendAlloutputToLog);
    addCommand("\n");

    // copy the resutls back
    addCommand(
        "cp "
            + localQualimapReport.getAbsolutePath()
            + " "
            + qualimapReport.getAbsolutePath()
            + appendAlloutputToLog);
    addCommand("\n");

    // remove the tmp dir from the sge host
    addCommand("rm -rf " + tmpDir.getAbsolutePath() + appendAlloutputToLog);
    addCommand("\n");
    addCommand("echo finished " + appendAlloutputToLog);
    addCommand("date " + appendAlloutputToLog);
  }
Ejemplo n.º 2
0
  public QualimapJob(File bam, File qualimapReport, GlobalConfiguration gc, String hostNameArg)
      throws IOException {
    super(FilenameUtils.removeExtension(bam.getAbsolutePath()) + "_qualimap.sh");
    this.bam = bam;
    this.qualimapReport = qualimapReport;
    this.gc = gc;

    sgeName = "qualimap_" + bam.getName();

    hostName = hostNameArg;
    this.sgeThreads = 8;

    sgeThreads = gc.getQualimapSGEThreads();

    addCommands();
    close();
  }