On Tue, Oct 12, 2010 at 7:44 AM, Freddy <freddy.debree@wur.nl> wrote:
Hi all,
Anybody some suggestions for this? Should I learn how to use rpy or simply stick with perl to get R running in galaxy.
I've been browsing through the existing tool scripts in the galaxy dist, but basically everything is written in rpy to run R tools. There's 2 things I could do: either run R through perl scripts or learn rpy, which looks pretty simple at first glance.
Freddy
Hi Freddy, It sounds like you know R already, but do you know Python? ;) I would agree rpy is pretty simple, and following the existing convention of using Python and rpy would make it easier for other Galaxy developers to understand/reused/change your script. However, rpy is no longer actively maintained and at some point Galaxy will need to move to rpy2 which is more flexible but not backwards compatible. See: http://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-v... As an alternative, how about just using R to write the script, and calling it directly from the Galaxy tool XML file? You can do command line parsing in R, right? You might find that simpler if you know R well. Peter