diff --git a/README.md b/README.md index fc7d6871..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` | `s3fs` or `cvmfs`, determines the CSI to use for mounting reference data. `s3fs` 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/templates/deployment-celery-beat.yaml b/galaxy/templates/deployment-celery-beat.yaml index 0f46248d..28795db7 100644 --- a/galaxy/templates/deployment-celery-beat.yaml +++ b/galaxy/templates/deployment-celery-beat.yaml @@ -139,8 +139,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} diff --git a/galaxy/templates/deployment-celery.yaml b/galaxy/templates/deployment-celery.yaml index 100b4ac6..5eb27cca 100644 --- a/galaxy/templates/deployment-celery.yaml +++ b/galaxy/templates/deployment-celery.yaml @@ -139,8 +139,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} diff --git a/galaxy/templates/deployment-job.yaml b/galaxy/templates/deployment-job.yaml index 29988bd1..0b77a89b 100644 --- a/galaxy/templates/deployment-job.yaml +++ b/galaxy/templates/deployment-job.yaml @@ -146,8 +146,8 @@ spec: {{- if $.Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq $.Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} diff --git a/galaxy/templates/deployment-web.yaml b/galaxy/templates/deployment-web.yaml index 783d1a52..c6be57bc 100644 --- a/galaxy/templates/deployment-web.yaml +++ b/galaxy/templates/deployment-web.yaml @@ -134,8 +134,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} diff --git a/galaxy/templates/deployment-workflow.yaml b/galaxy/templates/deployment-workflow.yaml index b994fbc9..4d744214 100644 --- a/galaxy/templates/deployment-workflow.yaml +++ b/galaxy/templates/deployment-workflow.yaml @@ -143,8 +143,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} diff --git a/galaxy/templates/jobs-init.yaml b/galaxy/templates/jobs-init.yaml index 92079e07..b78903bc 100644 --- a/galaxy/templates/jobs-init.yaml +++ b/galaxy/templates/jobs-init.yaml @@ -79,8 +79,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} @@ -187,8 +187,8 @@ spec: {{- if .Values.refdata.enabled }} - name: refdata-gxy mountPath: /cvmfs/data.galaxyproject.org - subPath: data.galaxyproject.org {{- if eq .Values.refdata.type "cvmfs" }} + subPath: data.galaxyproject.org # CVMFS automount volumes must be mounted with HostToContainer mount propagation. mountPropagation: HostToContainer {{- end }} 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