Step-class              Methods for Step objects
Utils                   Functions for directory operations
graphMng                Step graph management
initPipeFrame           initialize the pipeFrame package
runWithFinishCheck      Install dependent data or software with
                        finishing check
setGenome               Configure genome for all steps
setJobName              Configure the job name for following steps.
setRefDir               Set the reference directory
setThreads              Configure the maximum number of threads
setTmpDir               Configure the directory for intermediate
                        results of all steps
