Hi,
Thanks for your help.
I am able to run the jobs using the wrapper script but the problem is that instead of getting the stdout msg on the main screen panel
I am getting the message on the green panel (on the right )that displays the output files.
Here is the script that I wrote:
/usr/local/bin/kelvin-0.38.0 $1 --PedigreeFile $2 --MapFile $3 --FrequencyFile $4 --LocusFile $5 --BayesRatioFile $6 --PPLFile $7 --MODFile $8 2>&1
if [ "$?" = "0" ]
then
exit 0
#echo "Script executed successfully "
else
exit 1
#echo "Script failed"
fi
Thanks .
Regards,
Amit Modi
On 4/21/10 2:17 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Modi, Amit wrote:
> Hi,
>
> So a small question would galaxy recognize the job failure in case of no
> std error message and unsuccessful exit code
>
> Or it relies only on the std error for checking the successful /
> unsuccessful job completion.
This is the case. At present, only stderr matters, return codes are
always ignored. See the followup message by Assaf Gordon for a wrapper
that will do exactly what you need.
>
> Regards,
> Amit Modi
>
> On 4/21/10 1:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
>
> Modi, Amit wrote:
> > Hi ,
> >
> > Thanks a lot for the prompt reply.
> >
> > Our tool in the normal course of execution produce messages on both
> > stdout and stderr.But exits with a success status when successfully
> > executed
> >
> > So, does that means galaxy will always interpret this as job failure .
>
> In this case, yes.
>
> >
> > Is there any work around for this ?
>
> The simplest solution is a small wrapper that will suppress the messages
> from stderr. We've found that applications may not set a non-zero exit
> code upon failure, so looking for things written to stderr is the most
> reliable method for detecting failure.
>
> Since this is your own app and you know it sets proper return codes, the
> best thing to do would be to suppress stderr if the program returns 0,
> otherwise, print them as usual.
>
> --nate
>
> >
> > Regards,
> > Amit Modi
> >
> >
> >
> >
> > On 4/21/10 1:13 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
> >
> > Modi, Amit wrote:
> > > Hi,
> > >
> > > I am almost done with integrating our tool with galaxy.
> > >
> > > It would be really great if you can help solve this issue
> as I was
> > > unable find anything related to this on the wiki.
> > >
> > > Our tool produces some output messages during its execution
> due to
> > some
> > > reason galaxy splits them into 2 categories and displays as
> additional
> > > output and error messages though both of them are standard
> output
> > > messages ad should be displayed as additional output .
> > >
> > >
> > > Here is the snapshot of the message that is displayed.
> > >
> > > *Dataset 52: PPL File
> > > *
> > > Tool execution generated the following error message:
> > > 10/04/21 12:14:26 @0s, Initializing
> > > 10/04/21 12:14:26 @0s, Performing analysis
> > > 10/04/21 12:14:30 @4s, Analysis complete
> > > 10/04/21 12:14:30 @4s, Finished run
> >
> > Hi Amit,
> >
> > Are you sure that these messages are being printed to stdout?
> Galaxy
> > seems to be reading them from stderr.
> >
> > --nate
> >
> > >
> > > The tool produced the following additional output:
> > > 10/04/21 12:14:26 Use segment ID 4620291 for diagnostic
> purposes
> > > 10/04/21 12:14:26 kelvin V0.38.0 edit 2805 built Mar 25
> 2010 12:13:28
> > > 10/04/21 12:14:26 Compiler 4.1.1 20070105 (Red Hat 4.1.1-52)
> > > 10/04/21 12:14:26 Using GNU Scientific Library (GSL)
> statistical
> > > functions instead of internal ones
> > > 10/04/21 12:14:26 OpenMP-enabled w/maximum of 4 thread(s).
> > > 10/04/21 12:14:26 GCC optimization level 2 enabled
> > > 10/04/21 12:14:26 To check status (at some risk), type
> CTRL-\ or type
> > > "kill -3 28022"
> > > 10/04/21 12:14:26 Using configuration file
> > >
> /export/home/galaxy/galaxy-dist/database/files/000/dataset_151.dat
> > > 10/04/21 12:14:26 Computation is done in polynomial mode
> > > 10/04/21 12:14:26 polynomialScale is 1 (1-10, 1 is default)
> > > 10/04/21 12:14:26 Integration is done numerically (dkelvin)
> > > 10/04/21 12:14:26 Further progress will be displayed at 120
> second
> > intervals
> > > 10/04/21 12:14:26 9 pair(s) over a dynamic space (1LC) for 11
> > pedigree(s)
> > > 10/04/21 12:14:26 Trait-to-marker Two-Point, Dichotomous Trait,
> > Equilibrium.
> > > 10/04/21 12:14:30 stopwatch overall(1) e:4s u:8s s:1s,
> vx:205780,
> > > ivx:15961, sf:14225, hf:0
> > >
> > >
> > > Also, the tool executes just fine and also produces the
> correct output
> > > files.
> > >
> > > I can verify these files by looking into the
> > > galaxy/galaxy-dist/database/files/000/ directory.
> > >
> > >
> > > But for some reason these files are not displayed on the web
> > interface
> > > of galaxy and this error message is displayed along with failed
> > status.
> > >
> > > Thanks a lot.
> > >
> > > Regards,
> > > Amit Modi
> > >
> > >
> > > On 4/19/10 11:34 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
> > >
> > > Modi, Amit wrote:
> > > > Hi,
> > > >
> > > >
> > > > We are trying to configure Galaxy to work with our tool.
> > > >
> > > > So far I have been able to configure it well and link it
> > with the
> > > > cluster to do process all the jobs as per the
> documentation .
> > > >
> > > > Now what we want is the before the actual processing
> starts the
> > > > validations for the input files are done on the
> > > > Local. And the job processing is done on the cluster.
> > > >
> > > > Is there anyway we can configure this.
> > > >
> > > > We are using sge on the cluster.
> > >
> > > Hi Amit,
> > >
> > > I'm not sure what you mean by input file validation?
> You can have
> > > metadata set on the cluster by setting
> > 'set_metadata_externally = True'
> > > in the config file. Additionally, the data source
> tools like
> > Upload and
> > > UCSC can run on the cluster, providing the following
> are true:
> > >
> > > 1. The default directory used by Python's tempfile
> module is
> > > cluster-accessible (usually /tmp, so you can change it by
> > setting $TEMP
> > > in the environment).
> > >
> > > 2. The cluster nodes have access to the Internet (NAT
> is fine).
> > >
> > > If this is not what you're looking for, please let us know.
> > >
> > > --nate
> > >
> > > >
> > > > Thanks a lot.
> > > >
> > > >
> > > >
> > > > Regards,
> > > > Amit Modi
> > > >
> > > >
> > >
> >
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