[galaxy-dev] rpy or perl
peter at maubp.freeserve.co.uk
Tue Oct 12 04:51:19 EDT 2010
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.
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However, rpy is no longer actively maintained and at some point Galaxy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
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.
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