RDP’s Command Line Tools for Sequence Processing

I have written these exercises to run interactively using scripts that may be configured to run on a local installation of RDPTools or on MSU’s computer cluster. The scripts begin with configuration blocks that give the paths to necessary programs. Comment out the configuration blocks you do not need by inserting pound signs (#) at the beginning of the lines. The scripts include appropriate paths for MSU’s HPCC and for an installation made following the tutorial on installing RDTools on this web site. Otherwise, the paths for a local installation may need to be edited to conform with your particular installation. This will become clearer to you as you work through the exercises.

Running the exercises interactively is practical because the data sets are very small and therefore the programs take at most a few minutes to run. Real experiments may take hours or even days to run, in which case submitting jobs to a cluster is more practical. I will include some instructions for using MSU’s HPCC that may also give guidance in using computer clusters at other institutions.