[galaxy-dev] Galaxy issue

Modi, Amit Amit.Modi at nationwidechildrens.org
Wed Apr 21 13:35:16 EDT 2010


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 .

Is there any work around for this ?

Regards,
Amit Modi




On 4/21/10 1:13 PM, "Nate Coraor" <nate at 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 at 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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