shameless self-plug: we break out of R to do this, and after many painful
years developing and maintaining idiosyncratic Makefiles, we are now using
Taverna to (visually) glue together UNIX commands (including R scripts) --
the benefits of which (over make and brethren) is that you can actually
*see* the dependencies and overall workflow (nesting workflows also makes
it easier to manage complexity).

see TavernaPBS:

  http://cphg.virginia.edu/mackey/projects/sequencing-pipelines/tavernapbs/

while designed to automate job submission to a PBS queuing system, you can
also use it to simply execute non-PBS jobs.

--
Aaron J. Mackey, PhD
Assistant Professor
Center for Public Health Genomics
University of Virginia
amackey@virginia.edu
http://www.cphg.virginia.edu/mackey


On Thu, Apr 19, 2012 at 3:27 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> There are numerous tools like scons, make, ruffus, ant, rake, etc.
> that can be used to build complex pipelines based on task
> dependencies.  These tools are written in a variety of languages, but
> I have not seen such a thing for R.  Is anyone aware of a package
> available?  The goal is to be able to develop robust bioinformatic
> pipelines driven by scripts written in R.
>
> Thanks,
> Sean
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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