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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