Exiting a java application without errors
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Mikel Egaña Aranguren, PhD http://mikeleganaaranguren.com Marie Curie post-doc at Ontology Engineering Group, UPM http://www.oeg-upm.net/
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" <megana@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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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 and other Galaxy lists, please use the interface at:
participants (3)
-
Fields, Christopher J -
graham etherington (TSL) -
Mikel Egaña Aranguren