diff --git a/README.md b/README.md index 19ae3df3..d7384f17 100644 --- a/README.md +++ b/README.md @@ -162,7 +162,7 @@ current default values can be found in `values.yaml` file. | `jobs.rules` | Galaxy dynamic job rules. See `values.yaml` | | `jobs.priorityClass.existingClass` | Use an existing [priorityClass](https://kubernetes.io/docs/concepts/configuration/pod-priority-preemption/#priorityclass) to assign if `jobs.priorityClass.enabled=true` | | `refdata.enabled` | Whether or not to mount cloud-hosted Galaxy reference data and tools. | -| `refdata.type` | `s3csi` or `cvmfs`, determines the CSI to use for mounting reference data. `s3csi` is the default and recommended for the time being. | +| `refdata.type` | `s3csi` or `cvmfs`, determines the CSI to use for mounting reference data. `cvmfs` is the default type for reference data. | | `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. | | `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 | diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 6da949fd..73f7cef6 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -419,7 +419,7 @@ postgresql: refdata: #- Whether or not to mount cloud-hosted Galaxy reference data and tools. enabled: true - #- `s3fs` or `cvmfs`, determines the CSI to use for mounting reference data. + #- `s3csi` or `cvmfs`, determines the CSI to use for mounting reference data. #-`cvmfs` is the default and recommended for the time being. type: cvmfs pvc: @@ -477,7 +477,11 @@ configs: {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r, {{- template "galaxy.pvcname" . -}}/shed_tools:{{ .Values.persistence.mountPath -}}/shed_tools:r {{- if .Values.refdata.enabled -}} + {{- if eq .Values.refdata.type "cvmfs" -}} ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r + {{- else -}} + ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc:/cvmfs/data.galaxyproject.org:r + {{- end -}} {{- end -}} {{- if .Values.setupJob.downloadToolConfs.enabled -}} ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}:r