2011/9/15 Mikel Egaña Aranguren <meg...@fi.upm.es>:
> Hi;
>
> I'm sure this has been mentioned before but perhaps it has been fixed.
>

Not yet, but you can follow this issue:
https://bitbucket.org/galaxy/galaxy-central/issue/325/

> I'm writting a wrapper of a Java tool for Galaxy. The tool throws info to
> stderr even when working properly, and Galaxy interprets it as a bug. Is
> there any way of redirecting stderr (It seems that normal UNIX redirection
> to a file does not work) or making Galaxy ignore it?

I think redirection of stderr to /dev/nul should work fine,
remember to use the HTML escaping for the greater than.

The usual solution is a wrapper script which captures stderr,
and checks the return code for an error condition. e.g. Look
at the NCBI BLAST+ wrappers.

Peter

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