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[WIP] Test GCS packaged in new GKM #35

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[WIP] Test GCS packaged in new GKM #35

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2 changes: 1 addition & 1 deletion galaxykubeman/Chart.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ apiVersion: v1
appVersion: 21.09
description: A chart for deploying and managing a single Galaxy out-of-the-box instance on Managed Kubernetes clusters (GKE)
name: galaxykubeman
version: 1.2.0
version: 1.3.0
6 changes: 5 additions & 1 deletion galaxykubeman/requirements.yaml
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Expand Up @@ -8,5 +8,9 @@ dependencies:
version: 1.6.0
alias: cvmfs
- name: galaxy
repository: https://raw.githubusercontent.com/cloudve/helm-charts/anvil/
repository: https://raw.githubusercontent.com/almahmoud/helm-charts/anvil-gcs/
version: 4.8.0
- name: csi-gcs
repository: https://raw.githubusercontent.com/almahmoud/helm-charts/anvil-gcs/
version: 0.8.0
alias: gcs
7 changes: 7 additions & 0 deletions galaxykubeman/templates/_helpers.yml
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Expand Up @@ -44,3 +44,10 @@ Get default value or max
{{- .default | int }}
{{- end }}
{{- end }}

{{/*
Get bucket name from gcs uri
*/}}
{{- define "galaxykubeman.getBucketName" -}}
{{ .Values.configs.WORKSPACE_BUCKET | replace "gs://" "" }}
{{- end }}
38 changes: 38 additions & 0 deletions galaxykubeman/templates/gcs-resources.yaml
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@@ -0,0 +1,38 @@
apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
name: {{ .Release.Name }}-csi-gcs-sc
provisioner: {{ .Values.gcs.driverName }}
---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: {{ .Release.Name }}-csi-gcs-pvc
spec:
accessModes:
- ReadWriteMany
resources:
requests:
storage: 5Gi
storageClassName: {{ .Release.Name }}-csi-gcs-sc
---
apiVersion: v1
kind: PersistentVolume
metadata:
name: {{ .Release.Name }}-csi-gcs-pv
spec:
accessModes:
- ReadWriteMany
capacity:
storage: 5Gi
persistentVolumeReclaimPolicy: Retain
storageClassName: {{ .Release.Name }}-csi-gcs-sc
csi:
driver: {{ .Values.gcs.driverName }}
volumeHandle: csi-gcs
volumeAttributes:
gid: "101"
uid: "101"
bucket: '{{ include "galaxykubeman.getBucketName" . }}'
billingProject: "{{ .Values.configs.GOOGLE_PROJECT }}"
---
32 changes: 26 additions & 6 deletions galaxykubeman/values.yaml
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Expand Up @@ -7,6 +7,9 @@ configs: {}
secrets: {}
# db-password: changeme

gcs:
driverName: gcs.csi.ofek.dev

restore:
persistence:
nfs:
Expand Down Expand Up @@ -66,6 +69,14 @@ cvmfs:
enabled: false

galaxy:
extraVolumes:
- name: galaxy-remote-data
persistentVolumeClaim:
claimName: "{{ .Release.Name }}-csi-gcs-pvc"
extraVolumeMounts:
- mountPath: /galaxy/server/database/objects
name: galaxy-remote-data
subPath: galaxy-data/objects
jobs:
maxRequests:
cpu: 10
Expand Down Expand Up @@ -361,6 +372,7 @@ galaxy:
</toolbox>
galaxy.yml:
galaxy:
outputs_to_working_directory: true
job_config_file: "/galaxy/server/config/job_conf.yml"
enable_beta_gdpr: true
job_conf.yml:
Expand All @@ -376,19 +388,27 @@ galaxy:
k8s_pod_retries: "4"
k8s_walltime_limit: "604800"
k8s_galaxy_instance_id: "{{ .Release.Name }}"
k8s_persistent_volume_claims: |-
k8s_data_volume_claim: |-
{{ .Release.Name }}-csi-gcs-pvc/galaxy-data:{{ .Values.persistence.mountPath -}}
k8s_working_volume_claim: |-
{{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
k8s_persistent_volume_claims: |-
{{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
{{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config,
{{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps,
{{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache,
{{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp,
{{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data,
{{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools,
{{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index
{{- if .Values.cvmfs.enabled -}}
{{- range $key, $entry := .Values.cvmfs.galaxyPersistentVolumeClaims -}}
,{{- template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}}
,{{ template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}}
{{- end -}}
{{- end -}}
{{- if .Values.initJob.downloadToolConfs.enabled -}}
,{{ template "galaxy.pvcname" . -}}/{{ .Values.initJob.downloadToolConfs.volume.subPath }}:{{ .Values.initJob.downloadToolConfs.volume.mountPath -}}
{{- end -}}
{{- if .Values.extraVolumes -}}
{{- template "galaxy.extra_pvc_mounts" . -}}
{{- end }}
{{- end d}}
#k8s_timeout_seconds_job_deletion: 30
k8s_run_as_user_id: "101"
k8s_run_as_group_id: "101"
Expand Down