Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    robertbeudeker
    @robertbeudeker
    @nuwang Thanks for the suggestion, I will look into that. Question about that. KeyCloak is not mentioned as a supported provider in Galaxy(https://galaxyproject.org/authnz/config/oidc/). How do you connect keycloak to Galaxy?
    Nuwan Goonasekera
    @nuwang
    Keycloak is the same as custos. You can specify “Custos” as the IDP provider and point to your server settings. Additionally specify the realm as in this example: https://github.com/galaxyproject/cloudlaunch-registry/blob/6c8d92ba9b9bc8b9ae11721143211b9ce931e282/app-registry.yaml#L2531
    robertbeudeker
    @robertbeudeker
    @nuwang Thank you verry much. I indeed managed to setup a working test with Keycloak an AzureAD.
    Nuwan Goonasekera
    @nuwang
    np!
    Martin Cech
    @martenson
    Hi folks, I am trying to udnerstand how container mapping works with Galaxy on k8s. Is there some sort of summary that explains this mapping?
    Enis Afgan
    @afgane
    There’s no summary (yet) but it’s hopefully relatively self-explaining. It’s defined here: https://github.com/galaxyproject/galaxy-helm/blob/e9167da89481c6ba3db39bb75d524a315f6dae09/galaxy/values.yaml#L390 where you just say for what tool id, which container to use. That’s the mapping itself, or are you trying to understand the logic of the method you’ve linked?
    Nuwan Goonasekera
    @nuwang
    There’s no documentation as such, this sample file is the closest we have I think: https://github.com/galaxyproject/galaxy-helm/blob/e9167da89481c6ba3db39bb75d524a315f6dae09/galaxy/values.yaml#L389
    Martin Cech
    @martenson
    Nuwan Goonasekera
    @nuwang
    yes
    Martin Cech
    @martenson
    If there is no explicit hit in any of these k8s custom configs - the default is the container specified in tool xml requirements?
    (which is generally the Galaxy container)
    Nuwan Goonasekera
    @nuwang
    And if there’s no explicit mapping, Galaxy’s default mulled container resolution will apply
    Martin Cech
    @martenson
    So even if the tool specifies its own docker container, that will never be used in k8s?
    (unless explicitly configured through container_mapper_rules)
    Nuwan Goonasekera
    @nuwang
    container_mapper_rules only overrides. Otherwises, Galaxy’s defaults are what applies
    Enis Afgan
    @afgane
    I actually didn’t know a tool can specify its own container. Where does that happen?
    Enis Afgan
    @afgane
    Thanks. As Nuwan said, if the (override) mapping is not defined in the helm chart, Galaxy’s resolution should apply.
    Martin Cech
    @martenson
    So what happens if the resolution hits the container defined in the requirement?
    Is it going to riun that container in k8s?
    Enis Afgan
    @afgane
    Yes.
    Martin Cech
    @martenson
    Perfect, thank you.
    Martin Cech
    @martenson
    I have some more questions about k8s data persistence and handling. Is there something I should read before asking?
    In common deployments you either use nfs or Pulsar to stage in/out. Is Galaxy k8s different?
    Nuwan Goonasekera
    @nuwang
    It’s using NFS at the moment, but the plan is to migrate fully to Pulsar as the default (once Pulsar's remote object fetching is fully tested and ready)
    Martin Cech
    @martenson
    So in that way the Galaxy through Helm mimics the common deployment (file_path on NFS)?
    Nuwan Goonasekera
    @nuwang
    yes
    Martin Cech
    @martenson
    Alright, splendid. Thank you both.
    (And thanks for joining committers Nuwan :tada: )
    Nuwan Goonasekera
    @nuwang
    Np and glad to!
    I'm trying to figure out how to set cpu and memory limits and I assume it's done there?
    This seems like it probably shouldn't return a dict if default_resource_set is unset: https://github.com/galaxyproject/galaxy-helm/blob/master/galaxy/files/rules/k8s_container_mapper.py#L68
    Nate Coraor
    @natefoo
    Nuwan Goonasekera
    @nuwang
    @natefoo Did you run into an issue?
    Nate Coraor
    @natefoo
    I don't think there's a way to set any of these (or the walltime) for Pulsar coexecution pods
    Nuwan Goonasekera
    @nuwang
    Luke and I were just talking about that the other day. A lot of these options in the k8s runner will need to be ported over
    Nate Coraor
    @natefoo
    Yep
    Can I get kubectl describe (or another command) to output a spec? I don't see an option for it
    ah get ... -o yaml
    I'll test on Test
    Ghost
    @ghost~5772e7e2c2f0db084a206e1b
    Before replicating all this between Galaxy and pulsar in slightly different ways it might be a good idea to converge this in pulsar, and maybe make all of this templateable ?
    Longer term ofc
    Nuwan Goonasekera
    @nuwang
    Yes, that would be good. There was a preliminary attempt at this which was abandoned pending the shift to Pulsar, but perhaps the template etc. can still be used? galaxyproject/galaxy#10714
    Nate Coraor
    @natefoo
    pfft copy paste is the best method ;D