jobs not running with galaxy.yml

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jobs not running with galaxy.yml

Matthias Bernt
Dear list,

I'm trying to switch from galaxy.ini to yml on my dev instance (using a
drmaa runner starting jobs as real user). Somehow my jobs are not
starting anymore (it seems that they are not given to the job handler).
The only output I get is: INFO 2018-06-27 13:11:37,445 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Handled output named output for tool idba_ud
(25965.752 ms) INFO 2018-06-27 13:11:37,459 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Added output datasets to history (13.657 ms) INFO 2018-06-27 13:11:37,484 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Verified access to datasets for
Job[unflushed,tool_id=idba_ud] (5.423 ms) INFO 2018-06-27 13:11:37,484 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Setup for job Job[unflushed,tool_id=idba_ud]
complete, ready to flush (25.058 ms) INFO 2018-06-27 13:11:37,522 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Flushed transaction for job
Job[id=4366,tool_id=idba_ud] (37.777 ms) DEBUG 2018-06-27 13:11:37,522 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Tool [idba_ud] created job [4366] (26050.612 ms) DEBUG 2018-06-27 13:11:37,538 [p:19863,w:1,m:0]
[uWSGIWorker1Core2] Executed 1 job(s) for tool idba_ud request:
(26075.593 ms)

In addition to manual conversion I tried the auto conversion using `make
config-convert` with the same result.

I also tried to validate the yml file:

make config-validate

but get only:

pykwalify.errors.RuleError: <RuleError: error code 4: Types do not
match: 'None' --> '<type 'str'>': Path:

Any ideas where I could start digging?



Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
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