diff --git a/README.md b/README.md index d7384f17..061de010 100644 --- a/README.md +++ b/README.md @@ -167,6 +167,7 @@ current default values can be found in `values.yaml` file. | `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.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 bbae4835..319c31e8 100644 --- a/VALUES.md +++ b/VALUES.md @@ -41,6 +41,7 @@ | 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 index f680f119..11178d85 100644 --- a/galaxy/templates/configmap-cvmfs-fix.yaml +++ b/galaxy/templates/configmap-cvmfs-fix.yaml @@ -1,3 +1,4 @@ +{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} --- apiVersion: v1 kind: ConfigMap @@ -17,3 +18,4 @@ data: 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 index 7e88b036..9ca1738b 100644 --- a/galaxy/templates/hook-cvmfs-fix.yaml +++ b/galaxy/templates/hook-cvmfs-fix.yaml @@ -1,4 +1,4 @@ -{{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} +{{- 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 @@ -37,4 +37,3 @@ spec: configMap: name: "{{ .Release.Name }}-configmap-cvmfs-fix" {{- end }} - diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 94700f13..13a02bf1 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -429,6 +429,8 @@ 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: "{{ $.Release.Name }}-cvmfs" cvmfscsi: cache: