Question: [Tool Config] How to enforce cleanup tasks (shell commands) on job cancelation
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gravatar for mrals89
2.6 years ago by
mrals8950
United States
mrals8950 wrote:

Hello,

I have a tool which submits a custom pipeline shell script to our SGE. When a user cancels these jobs in Galaxy, the SGE jobs persist. Are there any "cleanup" tags for the XML that can perform certain shell commands before the job is considered canceled? Thank you!

tool tool-config galaxy xml • 631 views
ADD COMMENTlink modified 2.4 years ago by jmchilton1.1k • written 2.6 years ago by mrals8950
0
gravatar for jmchilton
2.4 years ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

There is no such configuration point in Galaxy, you may wish consider creating an issue for this https://github.com/galaxyproject/galaxy/issues if you consider it important - but it seems very niche and I am not sure it would a project priority so working through it an opening a pull request would probably be better.

In general though, are these actions that you can just have a cron job do? It seems like that would be much cleaner than modifying Galaxy to adapt to your cluster with specific cleanup actions.

ADD COMMENTlink written 2.4 years ago by jmchilton1.1k
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