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.vandewey...@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.vandewe...@ua.ac.be > http://ua.ac.be/**cognitivegenetics <http://ua.ac.be/cognitivegenetics> > http://www.linkedin.com/pub/**geert-vandeweyer/26/457/726<http://www.linkedin.com/pub/geert-vandeweyer/26/457/726> > > ______________________________**_____________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/**search/mailinglists/<http://galaxyproject.org/search/mailinglists/> >
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