Hi Jason,

Thanks for sharing your solution(s).

For other alternatives for running R scripts, you (or your colleague)
might want to look into:

 * Rscript (comes installed with R (these days))
 * littler (http://code.google.com/p/littler/)

Also, there are some libraries that deal with parsing command line
arguments, such as:

 * http://cran.r-project.org/web/packages/getopt/index.html
 * http://cran.stat.auckland.ac.nz/web/packages/optparse/index.html

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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