[galaxy-dev] rpy or perl

[Freddy]

  You're right, Peter,
I know R very well and I can sort argv elements.

Indeed, I tried to run R scripts straight in galaxy without wrappers.
For some reason it didn't capture the script and what is not so clear to me
is how the input/output direction works in galaxy. I know how it works
in R and shell, but then in connection with galaxy is not clear.

I started using the wrapper that is in the dist (r_wrapper.sh)
But that only accepts the input file through galaxy as first argv element.
I tried adding output file variable etc to the shell script, but that 
doesn't work (so far).

Thus, I thought, let's see what people think of using rpy/rpy2.




On 10/12/2010 10:51 AM, Peter wrote:
> 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 However, rpy is no longer actively maintained and at some point Galaxy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
>