[galaxy-dev] rpy or perl

[Peter]

On Tue, Oct 12, 2010 at 7:44 AM, Freddy <freddy.debree at 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However, rpy is no longer actively maintained and at some point Galaxy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-version

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