The first option (wrapper) also gives one the opportunity to actually check for 
errors.

Chris

On Dec 22, 2011, at 2:21 AM, "Mikel Egaña Aranguren" <meg...@fi.upm.es> wrote:

> 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/
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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