diff --git a/README.md b/README.md index f346e2c6..bbd56576 100644 --- a/README.md +++ b/README.md @@ -151,7 +151,6 @@ current default values can be found in `values.yaml` file. | `refdata.type` | `s3csi` or `cvmfs`, determines the CSI to use for mounting reference data. `cvmfs` is the default type for reference data. | | `cvmfs.enabled` | Enable use of CVMFS in configs, and deployment of CVMFS Persistent Volume Claims for Galaxy | | `cvmfs.pvc.{}` | Persistent Volume Claim to deploy for CVMFS repositories. See `values.yaml` for examples. | -| `cvmfs.deployPostInstallFix` |Deploy the fix for Galaxy-CVMFS-CSI Helm Chart. | | `setupJob.ttlSecondsAfterFinished` | Sets `ttlSecondsAfterFinished` for the initialization jobs. See the [Kubernetes documentation](https://kubernetes.io/docs/concepts/workloads/controllers/ttlafterfinished/#ttl-controller) for more details. | | `setupJob.downloadToolConfs.enabled` | Download configuration files and the `tools` directory from an archive via a job at startup | | `setupJob.downloadToolConfs.archives.startup` | A URL to a `tar.gz` publicly accessible archive containing AT LEAST conf files and XML tool wrappers. Meant to be enough for Galaxy handlers to startup. | diff --git a/VALUES.md b/VALUES.md index 319c31e8..bbae4835 100644 --- a/VALUES.md +++ b/VALUES.md @@ -41,7 +41,6 @@ | refdata.type | `s3fs` or `cvmfs`, determines the CSI to use for mounting reference data. `cvmfs` is the default and recommended for the time being. | | cvmfs | Configuration block if `cvmfs` is used as `refdata.type` | | cvmfs.deploy | Deploy the Galaxy-CVMFS-CSI Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource | -| cvmfs.deployPostInstallFix| Deploy the fix for Galaxy-CVMFS-CSI Helm Chart. | | s3csi | Configuration block if `s3csi` is used as the `refdata.type` | | s3csi.deploy | Deploy the CSI-S3 Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource. | | useSecretConfigs | When this flag is set to true, all configs will be set in secrets, when it is set to false, all configs will be set in configmaps | diff --git a/galaxy/templates/configmap-cvmfs-fix.yaml b/galaxy/templates/configmap-cvmfs-fix.yaml deleted file mode 100644 index 11178d85..00000000 --- a/galaxy/templates/configmap-cvmfs-fix.yaml +++ /dev/null @@ -1,21 +0,0 @@ -{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} ---- -apiVersion: v1 -kind: ConfigMap -metadata: - name: {{ .Release.Name }}-configmap-cvmfs-fix - labels: - {{- include "galaxy.labels" . | nindent 4 }} -data: - cvmfs-fix.sh: | - sleep 10; - status=`kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` - while [ "$status" != "Running" ]; do - echo "Waiting on nodeplugin pod to enter 'Running' status. Currently '$status'."; - sleep 1; - status=`kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` - done && \ - echo "Deleting nodeplugin pods..." - kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o name | xargs kubectl -n {{ .Release.Namespace }} delete && \ - echo "Deleted nodeplugin pods." -{{- end }} diff --git a/galaxy/templates/hook-cvmfs-fix.yaml b/galaxy/templates/hook-cvmfs-fix.yaml deleted file mode 100644 index 9ca1738b..00000000 --- a/galaxy/templates/hook-cvmfs-fix.yaml +++ /dev/null @@ -1,39 +0,0 @@ -{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} ---- -# Include the code you want to run when both conditions are met -apiVersion: batch/v1 -kind: Job -metadata: - name: "{{ .Release.Name }}-post-install-cvmfs-fix-job" - labels: - {{- include "galaxy.labels" . | nindent 4 }} - annotations: - "helm.sh/hook": post-install - "helm.sh/hook-weight": "10" - "helm.sh/hook-delete-policy": hook-succeeded -spec: - ttlSecondsAfterFinished: 120 - template: - metadata: - name: "{{ .Release.Name }}-post-install-cvmfs-fix-job" - labels: - {{- include "galaxy.labels" . | nindent 8 }} - spec: - serviceAccountName: {{ include "galaxy.serviceAccountName" . }} - securityContext: - {{- toYaml .Values.securityContext | nindent 8 }} - restartPolicy: Never - containers: - - name: post-install-kubectl - image: bitnami/kubectl - command: - - "sh" - - "/script/cvmfs-fix.sh" - volumeMounts: - - name: kubectl-script - mountPath: "/script" - volumes: - - name: kubectl-script - configMap: - name: "{{ .Release.Name }}-configmap-cvmfs-fix" -{{- end }} diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 8ab1879d..18afbc9e 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -426,8 +426,6 @@ refdata: cvmfs: #- Deploy the Galaxy-CVMFS-CSI Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource deploy: true - #- Deploy the CVMF post install fix, - deployPostInstallFix: true storageClassName: "galaxy-cvmfs" #- Configuration block if `s3csi` is used as the `refdata.type`