On Tue, Oct 12, 2010 at 11:40 AM, Freddy <freddy.debree(a)wur.nl> wrote:
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
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
But I will give R-straight another good try.
I've tried the things you mentioned, but I guess I have never used the
Will let you know how that goes.
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.