> 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.
Ah, this would be ideal. If you can get this to work, it woul
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 opti
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 c
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 genera
