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Merge pull request #498 from NilsKrattinger/imrpove_cvmfs_fix_configu…
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…rability

Make CVMFS fix configurable
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nuwang authored Aug 13, 2024
2 parents 59145bf + 8723418 commit b2d7627
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -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 <a href="galaxy/values.yaml">`values.yaml`</a> 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. |
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1 change: 1 addition & 0 deletions VALUES.md
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Expand Up @@ -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 |
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2 changes: 2 additions & 0 deletions galaxy/templates/configmap-cvmfs-fix.yaml
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@@ -1,3 +1,4 @@
{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
---
apiVersion: v1
kind: ConfigMap
Expand All @@ -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 }}
3 changes: 1 addition & 2 deletions galaxy/templates/hook-cvmfs-fix.yaml
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@@ -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
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configMap:
name: "{{ .Release.Name }}-configmap-cvmfs-fix"
{{- end }}

2 changes: 2 additions & 0 deletions galaxy/values.yaml
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Expand Up @@ -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:
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