Ok, so you're running the old tip of -dist. There are a few new updates you can retrieve using `hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central`.
-Dannon On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer < geert.vandewey...@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.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://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/ >> > > > > -- > > 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.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726 > >
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