On Tue, Oct 12, 2010 at 10:43 AM, Freddy <freddy.debree(a)wur.nl> wrote:
Running R from xml is not so straight forward to me.
Is the interpreter "bash" or is it "R"?
then it should be running "R --vanilla --slave input < Rscript >
then it should be running ? smthg like "source(Rscript)"
Hope you can help...
Consider a simple R script, hello_world.R like this:
Then in Galaxy I think you'd need the default interpreter
("bash") and the command to be:
R --vanilla --file=hello_world.R --args "Args go here"
I'm assuming your script will write useful output to a
file, and stdout can be discarded.
However, what I originally had in mind was setting the
hash bang and executable bit with chmod so that you
can do this at the command line:
./hello_world.R "Args go here"
Once that works, calling it from Galaxy should be trivial.
I think one way to do this is with the little r package: