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galaxyproject / galaxy-helm

Minimal setup required to run Galaxy under Kubernetes
MIT License
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Upgrade Galaxy version to 23.0 #414

Closed afgane closed 1 year ago

afgane commented 1 year ago

The auto-built image doesn't work out of the box atm because the version of TPV is wrong (see https://github.com/galaxyproject/galaxy/pull/15647#issuecomment-1453926643), but using a manually built image confirms the upgrade is working.

There are two issues/discussion points I'd like to raise:

  1. Should we consider versioning the chart in some way that mimics the Galaxy versions? If not, should this PR invoke a major version bump on the chart or something else?
  2. The default TPV database seems too generous with the resources for many tools for smaller instances. This is particularly evident during the chart development lifecycle where it's difficult to get many jobs to run on small dev envs (eg, FastQC requests 8 CPUs). Perhaps we could add an ability in TPV to scale all the default resources by some factor that would then make the those resource requests more acceptable to a local environment?
nuwang commented 1 year ago

Documenting the discussion here for posterity.

  1. The general helm chart convention is to use appVersion to track the underlying app's version, and to use semantic versioning for the helm chart, so that the two can be independently versioned. Therefore, the key basis for whether the chart needs a major version bump would be whether the chart can be a) Smoothly upgraded without hiccups b) Has no breaking changes to the chart interface Therefore, this particular case would be a minor version bump, despite the major appVersion bump.

  2. We can probably using clamping as a workaround for this: https://total-perspective-vortex.readthedocs.io/en/latest/topics/tpv_by_example.html#clamping-resources In particular, development setups would have to set something like

    helm install .... --set jobs.rules.tpv_rules_local\.yml.destinations.k8s.max_cores=2
afgane commented 1 year ago

With https://github.com/galaxyproject/galaxy/pull/15710 that fixes TPV versioning, this is ready for review/merge.