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galaxyproject / galaxy-helm

Minimal setup required to run Galaxy under Kubernetes
MIT License
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On Helm upgrade, Galaxy default tools don't get updated from a new galaxy container #418

Closed pcm32 closed 1 year ago

pcm32 commented 1 year ago

On subsequent runs of helm upgrade... of the chart, when the galaxy image changes, the default tools in /galaxy/server/database/tools don't get updated from the newer ones in the container.

Also, there is a repeated /galaxy/server/database/tools/tools directory with the same default tools again.

Should this be added in the init-mounts perhaps?

pcm32 commented 1 year ago

if you point me to where it needs to happen I could attempt a PR, thanks.

nuwang commented 1 year ago

On startup, the Galaxy container copies the tools directory from the container into the tools folder: https://github.com/galaxyproject/galaxy-helm/blob/d5d43d19c38397963e4f659bd9e486ca737ecbfa/galaxy/templates/_helpers.tpl#L164

I'm guessing this is a matter of a missing trailing "/", and the nested tools directory contains the newer files?

ksuderman commented 1 year ago

I think that is exactly what is happening; since a directory is being copied (cp -r) a new tools directory is being created inside the existing tools/ directory. Another solution would be to remove the /tools from {{ .Values.persistence.mountPath}}

pcm32 commented 1 year ago

Cool, thanks for finding and addressing this!