Hi;

My interpretation is that your BioJava tool is sending normal information to stderr, and Galaxy interprets it as an error. The same happened to me with OPPL-Galaxy.


This is a well known bug (http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr). You have two options:

- Best option: Use a wrapper as described in the page just mentioned.

- Worse option: use UNIX redirection to redirect the stderr output of your tool to /dev/null. This is much quicker and easier to implement, but it is a bad solution since legit errors of your BioJava tool will be simply ignored (The process will simply stop). Something like this in your tool XML:

<command>java -jar ${__tool_data_path__}/shared/jars/your_tool.jar $input > $output 2>/dev/null</command>

Cheers

On az., 2011.eko aberen 21a 18:53, graham etherington (TSL) wrote:
Hi,
I've created a java app tested it from the command line and put it in the
shared/jars folder. It runs for a while and then the history item turns
red. If I view the dataset output though, everything is as should be, i.e.
the expected output from the tool is seen.
If I click on the view error 'bug' this is what I see:

"Tool execution generated the following error message:
                     21-Dec-2011 17:08:14
org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading
/home/galaxy/software/galaxy-central/database/files/012/dataset_12450.dat"

This is the output from org.biojava3.genome.parsers.gff and I have no way
of switching that off.
Can anyone suggest a way to handle this output so that it doesn't throw an
error. I need the output from this tool to use as input to other tools.
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601




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--
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com

Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/

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