Hi Jeremy,

Thanks for your quick response.

I'll try switching from using 'tools/plotting/r_wrapper.sh' from
Galaxy distribution, to my own wrapper using python, so I can use your
advice.

I still wonder if this is the best way to run R's scripts? I would
have thought there would be a simpler option. I wonder if
"r_wrapper.sh" could be improved to absorb stderr messages, I would
guess Bash has these capabilities.

Thanks,
Carlos

On Mon, Jan 30, 2012 at 1:41 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> Carlos,
>
> You'll want to have your wrapper collect output to stderr and report only if 
> the tool fails. See the Cufflinks/compare/diff wrappers for examples of how 
> this can be done.
>
> Good luck,
> J.
>
> On Jan 30, 2012, at 1:01 PM, Carlos Borroto wrote:
>
>> Hi all,
>>
>> I'm working on integrating cummeRbund[1] into Galaxy. This is a very
>> helpful tool for analysis and visualization of cuffdiff output.
>>
>> My problem is any text output from running R code, puts the galaxy
>> output in error state. Even if everything is working correctly and the
>> outputs are generated as intended. I tried this code from
>> 'tools/plotting/xy_plot.xml':
>> ## Setup R error handling to go to stderr
>> options( show.error.messages=F,
>>    error = function () { cat( geterrmessage(), file=stderr() ); q(
>> "no", 1, F ) } )
>>
>> But it didn't help. Even for loading the library I had to go with:
>> suppressPackageStartupMessages(library("cummeRbund"))
>>
>> Nothing else would work. Now the tool is outputting some messages
>> while running R functions, which is putting the output in galaxy in
>> error state. I'm thinking about asking the upstream developer to
>> provide a way to run the functions in the library in 'quite' mode. Is
>> there any other option?
>>
>> Right now I'm using the path of creating a R script in the XML file
>> and using r_wrapper.sh to run it. I tried first with rpy, as it would
>> give me more freedom, but cummeRbund use ggplot2 which seems to be
>> supported only on rpy2.
>>
>> [1]http://compbio.mit.edu/cummeRbund/
>>
>> Thanks in advance,
>> Carlos
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