/** Copy pipeline to project home */
  protected void initialize() throws InitializationFailedException {
    WLogger.info("Marc job " + getID() + " is attempting to initialize");
    // Create base directory and initialize process builder with command
    super.initialize();

    WLogger.info("Marc job " + getID() + " has initialized successfully");
  }
  public MarcJob(
      File projHome,
      String pathToConfigFile,
      String sampleName,
      String submitter,
      String fastq1,
      String fastq2) {

    this.setBaseDir(projHome);
    String command =
        "perl "
            + pathToMasterAligner
            + " -c "
            + pathToConfigFile
            + " -u "
            + submitter
            + " -r "
            + sampleName
            + " "
            + fastq1
            + " "
            + fastq2;
    setCommand(command);
    setSampleName(sampleName);
    setSubmitter(submitter);

    WLogger.info("Creating new Marc job with command : " + getCommand());
  }