Question: This tool was disabled before the job completed
0
gravatar for christophe.habib
2.2 years ago by
France
christophe.habib340 wrote:

Hello everyone,

I am working on a local instance of galaxy. I am using uswgi and 2 handlers, with htcondor. When I try to use new tools installed from toolshed Galaxy has a strange behaviour.

When I launch a job, in galaxy webpage I have this error :

This tool was disabled before the job completed.  Please contact your Galaxy administrator.

There is no error in uwsgi.log, but if I look in handler.log I can see this :

galaxy.jobs DEBUG 2016-06-09 12:34:57,421 (26184) Working directory for job is: /home/galaxy/Formation/galaxy/database/job_working_directory/026/26184
galaxy.jobs.handler WARNING 2016-06-09 12:34:57,421 (26184) Tool 'toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.0.0' removed from tool config, unable to run job
galaxy.datatypes.metadata DEBUG 2016-06-09 12:34:57,543 Cleaning up external metadata files
galaxy.jobs.handler ERROR 2016-06-09 12:34:57,565 (26184) Error checking job readiness

or

galaxy.jobs DEBUG 2016-06-09 12:45:31,451 (26185) Working directory for job is: /home/galaxy/Formation/galaxy/database/job_working_directory/026/26185
galaxy.jobs.handler WARNING 2016-06-09 12:45:31,451 (26185) Tool 'toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.3.1' removed from tool config, unable to run job
galaxy.datatypes.metadata DEBUG 2016-06-09 12:45:31,770 Cleaning up external metadata files
galaxy.jobs.handler ERROR 2016-06-09 12:45:31,792 (26185) Error checking job readiness

Also, sometimes these tools disappear from the tool menu on the left and it seems they are not available anymore. But when I refresh (several times) the galaxy webpage, they come back.

I don't really understand this behaviour, and I don't know where I should start to understand it. Do you have any idea ?

Thank you,

Christ

galaxy disabled readiness • 839 views
ADD COMMENTlink written 2.2 years ago by christophe.habib340
3
gravatar for christophe.habib
2.2 years ago by
France
christophe.habib340 wrote:

This problem can be solved by restarting Galaxy instance. I have no explanation about the reason why it happened in the first place. (Thanks to pvh_sa on irc).

ADD COMMENTlink written 2.2 years ago by christophe.habib340
4

This happens for tools that are installed on a Galaxy server with multiple web handlers because only the web server which handled the install request has its toolbox updated. You need to restart the Galaxy server in order to have the toolbox of all web and job handlers in sync.

ADD REPLYlink written 2.2 years ago by Nicola Soranzo70
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