Merge pull request #486 from bravo325806/fix_s3csi_path

Fix s3csi path & readme
galaxyproject · Aug 12, 2024 · 59145bf · 59145bf
2 parents 250f463 + 76404b0
commit 59145bf
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Showing 8 changed files with 13 additions and 9 deletions.
diff --git 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 <a href="galaxy/values.yaml">`values.yaml`</a>                                                                                                                                                                |
 | `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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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:
@@ -482,7 +482,11 @@ 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