On Tue, Oct 12, 2010 at 11:40 AM, Freddy <freddy.debree@wur.nl> wrote:
Exactly, That is what confused me.
Earlier I simply tried running it 'straight' and that didn't work so well. Later I saw the wrappers thanks to James Taylor, but then it simply didn't produce output. so basically, I thought, I'm having a problem with in/output, so system problems rahter than R itself.
Thus, I was puzzled that galaxy itself was never using ANY R-script and only rpy/xml. But I will give R-straight another good try. I've tried the things you mentioned, but I guess I have never used the "--file=Rscript" option. Will let you know how that goes.
Cheers, Freddy
As I understand it: * Galaxy will capture stdout/stderr (unless you have redirected them), stdout is discarded, and any text on stderr is treated as an error. * If you want output from a script, it should be sent to a file Since R tends to be very noisy on stdout, it is probably best to ignore stdout and make any output explicit to a file (whose name should be a command line argument which Galaxy will assign). Please keep us posted - I do sometimes write plain R scripts myself, although I have tended to use a Python script and rpy more often. Peter