Re: [galaxy-user] running R in Galaxy

On Tue, Sep 21, 2010 at 5:30 AM, Bree, Freddy de <freddy.debree@wur.nl>wrote:

I've been trying to run R in Galaxy.

1. Running it as "R" is a hassle, because Galaxy cannot deal with source and input file and output file using "--args" and "<" (< in xml) and ">" (> in xml).

2. Running it through "perl" is also a hassle, because Galaxy needs to have an input file through the cmd line, whilst "R" needs: - input file (the location of it, not the content) - source file (.R file) - output file BUT you need to pipe -this- input for perl through to R VIA the system() call.

Anybody any luck with this?

Have you tried littler as a scripting engine? http://dirk.eddelbuettel.com/code/littler.html That is only one potential solution. Sean