Hello,
On our Galaxy server (21.05), we enabled the option to prevent Galaxy from removing files from the jobs directory when the job fails, namely in galaxy.yml :
cleanup_job: onsuccess
After resolving the issues with failed jobs, we would like to remove the files remaining in the failed jobs directories, for instance
data/jobs_directory/029/29363/
How can we properly do that removal ?
(1) We have not found any possibility in the Galaxy web gui
(2) We tried to use Bioblend along with an admin key, however it seems there is no API to perform this cleanup. We tried to use gi.jobs.cancel_job(id) but it did not remove the files (https://github.com/galaxyproject/bioblend/blob/main/bioblend/galaxy/jobs/init.py#L305).
(3) We tried to use the Galaxy web REST API, with a DELETE request on /api/jobs/{id} along with an admin key, without success (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/jobs.py#L297).
(4) It seems, regarding https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/managers/jobs.py#L87 , that the job should be marked as “finished” for the stop() method to actually delete the files. We have however no idea how to mark an error job as finished.
Could you help us ?
Thanks !