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pcm32 / galaxy-helm-charts

Deployment of Galaxy on Kubernetes through Helm Charts
MIT License
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invalid resource error #5

Open jianlianggao opened 5 years ago

jianlianggao commented 5 years ago

Hi Pablo,

I am trying to deploy with minikube on Windows. helm install give errors like

Error: error validating "": error validating data: the server could not find the requested resource

kubectl logs show

[tiller] 2019/08/01 08:07:59 getStatus: Release name is invalid: galaxy-helm-repo/galaxy

What's happened?

Best wishes, Jianliang

pcm32 commented 5 years ago

Hi Jianliang,

This repo is rather old… did you add the repo to your local setup?

helm repo add galaxy-helm-repo https://pcm32.github.io/galaxy-helm-charts

Cheers, Pablo

On 1 Aug 2019, at 09:17, Jianliang notifications@github.com wrote:

Hi Pablo,

I am trying to deploy with minikube on Windows. helm install give errors like

Error: error validating "": error validating data: the server could not find the requested resource

kubectl logs show

[tiller] 2019/08/01 08:07:59 getStatus: Release name is invalid: galaxy-helm-repo/galaxy

What's happened?

Best wishes, Jianliang

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jianlianggao commented 5 years ago

Hi Pablo,

Yes, I did add the line.

[tiller] 2019/08/01 08:08:36 getStatus: Release name is invalid: galaxy-helm-charts/galaxy

jianlianggao commented 5 years ago

Hi Pablo,

Looks like it is back working now. I waited for a couple hours and reran the command line, it is pulling container image now. I will update with you for further information.

Many thanks, Best wishes, Jianliang

jianlianggao commented 5 years ago

Hi Pablo,

I got a pod running but I couldn't connect.

NAME               READY   STATUS    RESTARTS   AGE
galaxy-k8s-gk84g   1/1     Running   2          11m

C:\Users\Pillar>kubectl describe pods galaxy-k8s-gk84g
Name:           galaxy-k8s-gk84g
Namespace:      default
Priority:       0
Node:           minikube/10.0.2.15
Start Time:     Thu, 01 Aug 2019 14:32:41 +0100
Labels:         app=galaxy-k8s
Annotations:    <none>
Status:         Running
IP:             172.17.0.5
Controlled By:  ReplicationController/galaxy-k8s
Containers:
  galaxy-k8s:
    Container ID:  docker://3328111bf028d957947582bc60c713d4fb4804ab21adb5e804f6526b9a189dcd
    Image:         docker-registry.phenomenal-h2020.eu/phnmnl/galaxy-k8s-runtime:latest
    Image ID:      docker-pullable://docker-registry.phenomenal-h2020.eu/phnmnl/galaxy-k8s-runtime@sha256:12c2a5acc737261f802c6505a7b36a7f46fbc0bcb4ccce425441c6e432ee6742
    Port:          8080/TCP
    Host Port:     0/TCP
    Command:
      /bin/bash
      -c
      mkdir -p /opt/galaxy_data/database-sqlite && ./ansible/run_galaxy_config.sh > galaxy_config.log && ./run.sh --daemon && tail -f paster.log
    State:          Running
      Started:      Thu, 01 Aug 2019 14:41:42 +0100
    Last State:     Terminated
      Reason:       Error
      Exit Code:    1
      Started:      Thu, 01 Aug 2019 14:37:03 +0100
      Finished:     Thu, 01 Aug 2019 14:41:09 +0100
    Ready:          True
    Restart Count:  2
    Environment:
      TOOLS_DEST_PVC:  /opt/galaxy_data/
    Mounts:
      /galaxy/config/galaxy.ini from galaxy-ini (rw)
      /galaxy/config/job_conf.xml from galaxy-job-conf (rw)
      /galaxy/config/tool_conf.xml from galaxy-tool-conf (rw)
      /galaxy/tools/phenomenal from phenomenal-tools (rw)
      /opt/galaxy_data from galaxy-pvc (rw)
      /var/run/secrets/kubernetes.io/serviceaccount from default-token-k6z7v (ro)
Conditions:
  Type              Status
  Initialized       True
  Ready             True
  ContainersReady   True
  PodScheduled      True
Volumes:
  galaxy-pvc:
    Type:       PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
    ClaimName:  galaxy-pvc
    ReadOnly:   false
  galaxy-ini:
    Type:          HostPath (bare host directory volume)
    Path:          /c/Users/Pillar/container-galaxy-k8s-runtime-metaboflow/config/galaxy.ini
    HostPathType:
  galaxy-job-conf:
    Type:          HostPath (bare host directory volume)
    Path:          /c/Users/Pillar/container-galaxy-k8s-runtime-metaboflow/config/job_conf.xml
    HostPathType:
  galaxy-tool-conf:
    Type:          HostPath (bare host directory volume)
    Path:          /c/Users/Pillar/container-galaxy-k8s-runtime-metaboflow/config/tool_conf.xml
    HostPathType:
  phenomenal-tools:
    Type:          HostPath (bare host directory volume)
    Path:          /c/Users/Pillar/container-galaxy-k8s-runtime-metaboflow/tools/phenomenal
    HostPathType:
  default-token-k6z7v:
    Type:        Secret (a volume populated by a Secret)
    SecretName:  default-token-k6z7v
    Optional:    false
QoS Class:       BestEffort
Node-Selectors:  <none>
Tolerations:     node.kubernetes.io/not-ready:NoExecute for 300s
                 node.kubernetes.io/unreachable:NoExecute for 300s
Events:
  Type     Reason     Age                    From               Message
  ----     ------     ----                   ----               -------
  Normal   Scheduled  11m                    default-scheduler  Successfully assigned default/galaxy-k8s-gk84g to minikube
  Warning  BackOff    2m52s (x2 over 2m57s)  kubelet, minikube  Back-off restarting failed container
  Normal   Pulling    2m38s (x3 over 11m)    kubelet, minikube  Pulling image "docker-registry.phenomenal-h2020.eu/phnmnl/galaxy-k8s-runtime:latest"
  Normal   Pulled     2m37s (x3 over 11m)    kubelet, minikube  Successfully pulled image "docker-registry.phenomenal-h2020.eu/phnmnl/galaxy-k8s-runtime:latest"
  Normal   Created    2m32s (x3 over 11m)    kubelet, minikube  Created container galaxy-k8s
  Normal   Started    2m27s (x3 over 11m)    kubelet, minikube  Started container galaxy-k8s

C:\Users\Pillar>kubectl get pods
NAME               READY   STATUS    RESTARTS   AGE
galaxy-k8s-gk84g   1/1     Running   2          12m

Anything wrong?

Best wishes, Jianliang

jianlianggao commented 5 years ago

Hi Pablo,

I can't connect to 192.168.99.100:30700 and when I tried https://192.168.99.100:8443/ I have the following errors

{
  "kind": "Status",
  "apiVersion": "v1",
  "metadata": {

  },
  "status": "Failure",
  "message": "forbidden: User \"system:anonymous\" cannot get path \"/\"",
  "reason": "Forbidden",
  "details": {

  },
  "code": 403
}