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Fix s3csi path & readme #486

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merged 5 commits into from
Aug 12, 2024
Merged

Fix s3csi path & readme #486

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f23b51c
fix readme & remove s3csi subpath
Jul 11, 2024
857d081
update README
Jul 11, 2024
fffe806
Do not use subpath is refdata is using s3csi
ksuderman Aug 7, 2024
e3ab151
CVMFS is the default for reference data
ksuderman Aug 7, 2024
76404b0
Merge pull request #2 from ksuderman/fix_s3csi_path
bravo325806 Aug 12, 2024
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 |
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2 changes: 1 addition & 1 deletion galaxy/templates/deployment-celery-beat.yaml
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Expand Up @@ -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 }}
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2 changes: 1 addition & 1 deletion galaxy/templates/deployment-celery.yaml
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Expand Up @@ -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 }}
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2 changes: 1 addition & 1 deletion galaxy/templates/deployment-job.yaml
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Expand Up @@ -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 }}
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2 changes: 1 addition & 1 deletion galaxy/templates/deployment-web.yaml
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Expand Up @@ -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 }}
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2 changes: 1 addition & 1 deletion galaxy/templates/deployment-workflow.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
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4 changes: 2 additions & 2 deletions galaxy/templates/jobs-init.yaml
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Expand Up @@ -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 }}
Expand Down Expand Up @@ -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 }}
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6 changes: 5 additions & 1 deletion galaxy/values.yaml
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Expand Up @@ -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:
Expand Down Expand Up @@ -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
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