On Apr 17, 2013, at 9:11 AM, Ramon Tiburski wrote:

> Hi Nate, thank you for the help, I'm posting more details about the error, 
> Did you ever see something like this?

Hi Ramon,

Without being familiar with the tool, I am not sure what is happening here.  
Either the process of sourcing the env.sh file or calling cdo is failing, for 
unknown reasons.  It could be that the command is not being executed through a 
shell, in which case the source (',') and the join (';') specials would not be 
recognized.

--nate

> 
> Thank you so much,
> 
> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'ps': 
> 'module' object has no attribute 'scripts'
> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 
> 'galaxy.datatypes.scripts:PostScript' to sniff_order: No module named scripts
> INFO:NetCDFwithTimeAxis:NetCDFwithTimeAxis set_meta
> INFO:NetCDFwithTimeAxis:NetCDF set_meta
> INFO:NetCDFwithTimeAxis:Climate set_meta
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  infon /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  infon /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> Aborting.
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> Aborting.
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump
>  -x /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump
>  -x /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> Aborting.
> galaxy.jobs.runners.local DEBUG 2013-04-17 09:51:59,955 execution of external 
> set_meta for job 15 finished
> galaxy.jobs DEBUG 2013-04-17 09:51:59,979 Tool did not define exit code or 
> stdio handling; checking stderr for success
> galaxy.datatypes.metadata DEBUG 2013-04-17 09:52:00,029 setting metadata 
> externally failed for HistoryDatasetAssociation 15: External set_meta() not 
> called
> NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 NetCDFwithTimeAxis set_meta
> NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 NetCDF set_meta
> NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 Climate set_meta
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  infon /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  infon /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> Aborting.
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo
>  sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> Aborting.
> [localhost] local: . 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump
>  -x /home/ramao/galaxy/database/files/000/dataset_15.dat
> 
> Fatal error: local() encountered an error (return code 127) while executing 
> '. 
> /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump
>  -x /home/ramao/galaxy/database/files/000/dataset_15.dat'
> 
> 
> > Subject: Re: [galaxy-dev] Unable to finish job
> > From: n...@bx.psu.edu
> > Date: Tue, 16 Apr 2013 11:45:37 -0400
> > CC: galaxy-dev@lists.bx.psu.edu
> > To: ramao_tiago_tibur...@hotmail.com
> > 
> > On Apr 16, 2013, at 9:37 AM, Ramon Tiburski wrote:
> > 
> > > I,m getting this error when I try to convert some data, can someone help 
> > > me?
> > > 
> > > Traceback (most recent call last):
> > > File "/home/ramao/galaxy/lib/galaxy/jobs/runners/local.py", line 156, in 
> > > run_job
> > > job_wrapper.finish( stdout, stderr, exit_code )
> > > File "/home/ramao/galaxy/lib/galaxy/jobs/__init__.py", line 412, in finish
> > > dataset.datatype.set_meta( dataset, overwrite = False ) #call 
> > > datatype.set_meta directly for the initial set_meta call during dataset 
> > > creation
> > > File 
> > > "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py",
> > >  line 318, in set_meta
> > > NetCDF.set_meta(self,dataset)
> > > File 
> > > "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py",
> > >  line 261, in set_meta
> > > ncml= execAndGetStdout("ncdump -x "+dataset.file_name)
> > > File 
> > > "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py",
> > >  line 48, in execAndGetStdout
> > > output=local(cmd, capture=True)
> > > File 
> > > "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/operations.py", 
> > > line 1012, in local
> > > error(message=msg, stdout=out, stderr=err)
> > > File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", 
> > > line 305, in error
> > > return func(message)
> > > File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", 
> > > line 26, in abort
> > > sys.exit(1)
> > > SystemExit: 1
> > 
> > Hi Ramon,
> > 
> > For a definite answer, you'll want to contact the tool/datatype author. 
> > However, I would guess that the `ncdump` command is failing for some 
> > reason, and that would be the place to look.
> > 
> > --nate
> > 
> > > 
> > > ___________________________________________________________
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> >


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