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    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
    Marius van den Beek
    @mvdbeek
    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
    Nate Coraor
    @natefoo
    (yes, you're right, but if this works I'm PRing it anyway as I need it to work in production and we can refactor it later)
    Marius van den Beek
    @mvdbeek
    :+1:
    Nate Coraor
    @natefoo
    requests and limits work but activeDeadlineSeconds doesn't - this works on your regular (non-pulsar) k8s jobs @nuwang ?
    Nuwan Goonasekera
    @nuwang
    Yes. The job should stop, but it won’t get cleaned up
    or may not get cleaned up
    Nate Coraor
    @natefoo
    ahh the option is at the wrong level of the dict
    Nate Coraor
    @natefoo
    Nice, fixed
    Nate Coraor
    @natefoo
    Nuwan Goonasekera
    @nuwang
    :+1:
    Pablo Moreno
    @pcm32
    Hi, question @nuwang is it me or the docs in https://github.com/galaxyproject/galaxy-docker-k8s don’t really explain how to build that docker image? The repo doesn’t have a Dockerfile, yet all explanations are with docker build. I’m guessing you need to use the ansible playbook there, but it could be great if the readme would be explicit about what are those steps. Thanks!
    1 reply
    Gulsum Gudukbay
    @gulsumgudukbay
    Hi, I am following this tutorial: https://training.galaxyproject.org/training-material/topics/admin/tutorials/k8s-deploying-galaxy/tutorial.html#deploying-a-cvmfs-enabled-configuration to deploy Galaxy on k8s. However, when I reach the end of the tutorial and run "kubectl get pods", the pod "galaxy-metrics-scraper-9844bf959-8m8wk" has status "CreateContainerConfigError" and all the other pods are "Pending". To understand why this pod has the ConfigError, I checked the logs and there seems to be a problem with influxdb secret creation (Error: couldn't find key influxdb-user in Secret default/galaxy-galaxy-secrets). How can I solve this problem?
    Alexandru Mahmoud
    @almahmoud
    @pcm32 I replied to your issue in github
    Alexandru Mahmoud
    @almahmoud
    @gulsumgudukbay Could you give some more details on the type of environment you're deploying in? Is it on a managed k8s (gke, aks, eks, etc...) or a cluster you built yourself? Are you looking to deploy only 1 Galaxy or multiple ones in the same cluster? Are you looking to run a single-node or multi-node cluster? Do you have a shared filesystem eg NFS (you will need one if you have more than one node)? And finally what version of k8s are you running in, and what values did you change, if any?
    Those tutorials are a bit out of date since the defaults have changed in the charts. This might be more useful to you for a basic installation with CVMFS, but happy to help more for potential specific things for your use-case: https://github.com/galaxyproject/galaxy-helm/tree/2009readme#example-installation-for-a-single-galaxy-instance-with-cvmfs-tools
    Gulsum Gudukbay
    @gulsumgudukbay
    Hi @almahmoud I setup a k8s cluster that has 1 kubemaster and 1 node, and I want to deploy only 1 Galaxy instance on that cluster. It is a multi-node cluster. I also tried the CVMFS section of the tutorial and got the same error. The kube version is Major:"1", Minor:"20", GitVersion:"v1.20.4", for both nodes.
    I will try the github link you mentioned and let you know if there's any problem. Thanks!
    Alexandru Mahmoud
    @almahmoud
    Do you have a ReadWriteMany storage class? also I'm not sure if we've tested the chart with 1.20, there might be some api versions out of date or such things... Let me know how it goes though, i'd be happy to help start pushing to make it compatible with 1.20 if things don't work