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/
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