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@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 > > ------------------------------------------------------------------------ > > * ----------------------------------------- Confidentiality Notice: The > following mail message, including any attachments, is for the sole use > of the intended recipient(s) and may contain confidential and privileged > information. The recipient is responsible to maintain the > confidentiality of this information and to use the information only for > authorized purposes. If you are not the intended recipient (or > authorized to receive information for the intended recipient), you are > hereby notified that any review, use, disclosure, distribution, copying, > printing, or action taken in reliance on the contents of this e-mail is > strictly prohibited. If you have received this communication in error, > please notify us immediately by reply e-mail and destroy all copies of > the original message. Thank you. * > > > ------------------------------------------------------------------------ > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev