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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