Thanks again! This solves it I think. I re-directed this to galaxy-user, because it is clear that some of you do not know this either. ;) ________________________________________ From: James Taylor [james@jamestaylor.org] Sent: 21 September 2010 13:21 To: Bree, Freddy de Subject: Re: [galaxy-user] running R in Galaxy Yes, tools/stats/r_wrapper.sh On Sep 21, 2010, at 7:16 AM, Bree, Freddy de wrote:

Thanks for the tip, but do you mean in Galaxy?

________________________________________ From: James Taylor [james@jamestaylor.org] Sent: 21 September 2010 13:06 To: Bree, Freddy de Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] running R in Galaxy

On Sep 21, 2010, at 5:30 AM, Bree, Freddy de wrote:

...

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).

We use a small shell script called r_wrapper.sh which is included in the distribution.