Aside: If I add steps to the beginning of the workfow, the step that
runs too early, typically occurs earlier in the flow. Can this indicate
a race condition where not all dependencies are available (stored?) yet
in the database at the time of querying for job eligible for queueing?
Best,
Geert
On 05/21/2013 11:06 PM, Geert Vandeweyer wrote:
Hi Dannon,
I pulled the new updates and restarted galaxy. However, the issue is
not resolved. Is there other information you might need?
hg summary:
parent: 9332:0f51ae4f1c84 tip
Unicode fixes for workflow names in Tool Menu.
branch: stable
Best,
Geert
On 05/21/2013 06:08 PM, Dannon Baker wrote:
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`
<http://bitbucket.org/galaxy/galaxy-central%60>.
-Dannon
On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer
<[email protected] <mailto:[email protected]>> 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
<[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
___________________________________________________________
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:[email protected] <mailto:[email protected]>
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
--
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:
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: [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:
http://galaxyproject.org/search/mailinglists/
