On Wed, Apr 21, 2010 at 01:46:33PM -0400, Nate Coraor wrote:
The simplest solution is a small wrapper that will suppress the messages from stderr. We've found that applications may not set a non-zero exit code upon failure, so looking for things written to stderr is the most reliable method for detecting failure.
If you're employing a shell script wrapper around your tool in the tool runner, as many seem to do, you can just add "2>&1" to the end of your command. For example in the /galaxy-dist/tools/plotting/r_wrapper.sh file the line that looks like:
R --vanilla --slave $* < $infile
would change to
R --vanilla --slave $* < $infile 2>&1