On og., 2011.eko iraren 15a 20:40, Peter Cock wrote:
2011/9/15 Mikel Egaña Aranguren<meg...@fi.upm.es>:

I'm sure this has been mentioned before but perhaps it has been fixed.

Not yet, but you can follow this issue:

OK thanks

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.

Yes it works fine.

I haven't scaped the ">" character and it works fine (?)

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.

OK I will have a look

Thanks again



Mikel Egaña Aranguren, PhD

Marie Curie post-doc at Ontology Engineering Group, UPM

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