On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote:

hg summary:

parent: 9320:47ddf167c9f1 tip
Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response. Fixes downloading tarballs from the Tool Shed when use_debug = false.
branch: stable
commit: 18 modified, 178 unknown
update: (current)

Geert

On 05/21/2013 04:59 PM, Dannon Baker wrote:
Geert,

This should be fixed in the up-to-date stable branch as far as I know. Can you tell me what 'hg summary' states?

-Dannon

On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote:

Hi,

After the latest upgrade (april), I'm having issues when starting (batch) workfows. Sometimes, it seems that step dependencies are not stored correctly, leading to some steps being started too soon, without prior datasets being completed. Specifically, for some workflows, some of the later steps start immediately. The issue seems to be random: in batch workflow submission, some run flawlessly, others show the issue, at different steps. I use one handler in the job_conf to exclude race conditions and shared variable clashes.

I suspect there is an issue with fetching or storing the steps to/from the database (a remote mysql database in my case). On the mysql-side there are no errors in the log files, and the galaxy-logs don't show clear issues either.

Does the job new job handler check for failed database connections? If not, could somebody point me to the code that performs these steps, I'd like to add a check & retry routine to see if this improves the situation.

best,

Geert

--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 