/** 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());
}