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
<[email protected] <mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
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: [email protected]
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:
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