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?
That is only one potential solution.
Sean