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
>>
>> ___________________________________________________________
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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.vandewe...@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>
>
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