getObjsInPipe           Obtain all of objects in the specific pipeline
graphMng                Step graph management
ignoreCheck             ignore checking input and output file (for
                        developer)
initPipeFrame           initialize the pipeFrame package
loadConfig              load configure from file
loadStep                load step object from rds file
runWithFinishCheck      Install dependent data or software with
                        finishing check
setGenome               Configure genome for all steps
setJobName              Configure the job name for following steps.
setPipeName             Configure the pipe 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
Step-class              Methods for Step objects
Utils                   Functions for directory operations
