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

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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