On Tue, Oct 12, 2010 at 10:43 AM, Freddy freddy.debree@wur.nl wrote:
Hi Peter,
Running R from xml is not so straight forward to me. Is the interpreter "bash" or is it "R"? If "bash" then it should be running "R --vanilla --slave input < Rscript > output" if "R" then it should be running ? smthg like "source(Rscript)"
Hope you can help...
Freddy
Consider a simple R script, hello_world.R like this:
print('Hello world'); print(commandArgs());
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: http://code.google.com/p/littler/
Peter