/** 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()); }