Hi; On og., 2011.eko iraren 15a 20:40, Peter Cock wrote:

2011/9/15 Mikel Egaña Aranguren<megana@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/

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 Regards

Peter

-- Mikel Egaña Aranguren, PhD http://mikeleganaaranguren.com Marie Curie post-doc at Ontology Engineering Group, UPM http://www.oeg-upm.net/