[R] running multiple commands in one system() call

[Nick Matzke]

Hi all,

I'm on Mac OS X 10.4...

So I've got a small python script I need to run from R.  However, to get 
the python script working, I need to have the shell that R calls get 
settings from my .bash_profile file, which apparently it doesn't 
currently (the shell R calls uses an older version of python, and also 
this older version of python can't see various python modules I have to 
import to make the python script work).

Basically I need to do this:

============
mytreefile_location <- 
"/bioinformatics/phylocom/_results/beta/ss_newicks/subsamp6_fromea_wnalist.newick"

cmd1 = 'source ~/.bash_profile'
cmd2 = paste('python 
/bioinformatics/phylocom/_scripts/update_newick_root.py ', 
mytreefile_location)

system(cmd1)
system(cmd2)
============

...but if I do it this way, the sourcing of .bash_profile from the first 
system() call does not carry over to the 2nd system() call.


Any help appreciated!!

Cheers,
Nick



-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
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Department of Integrative Biology
University of California, Berkeley

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