Cron job maintenance

galaxy/templates/cronjob-maintenance.yaml

@@ -1,23 +1,26 @@
+{{- if .Values.maintenance.tmp.enabled }}
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance
+  name: {{ include "galaxy.fullname" . }}-maintenance-clean-tmp
   labels:
     {{- include "galaxy.labels" . | nindent 4 }}
 spec:
-  schedule: "0 2 * * *"
+  schedule: {{ .Values.maintenance.tmp.schedule | quote }}
   jobTemplate:
     spec:
       template:
         spec:
           securityContext:
+            runAsUser: 0
             {{- toYaml .Values.securityContext | nindent 12 }}
           {{- with .Values.nodeSelector }}
           nodeSelector:
             {{- toYaml . | nindent 16 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
+          - name: galaxy-maintenance-clean-tmp
             image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
             imagePullPolicy: {{ .Values.image.pullPolicy }}
             # delete all tmp files older than walltime limit
@@ -26,7 +29,7 @@ spec:
               - {{ .Values.persistence.mountPath }}/tmp
               - '!'
               - -newermt
-              - -{{ (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) }} seconds
+              - "{{ .Values.maintenance.tmp.seconds }} seconds"
               - -type
               - f
               - -exec
@@ -45,3 +48,102 @@ spec:
             emptyDir: {}
             {{- end }}
           restartPolicy: OnFailure
+{{- end }}
+{{- if .Values.maintenance.script.enabled }}
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "galaxy.fullname" . }}-maintenance-script
+  labels:
+    {{- include "galaxy.labels" . | nindent 4 }}
+spec:
+  schedule: {{ .Values.maintenance.script.schedule | quote }}
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          securityContext:
+            runAsUser: 0
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 16 }}
+          {{- end }}
+          containers:
+          - name: galaxy-maintenance-script
+            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+            imagePullPolicy: {{ .Values.image.pullPolicy }}
+            # delete all tmp files older than walltime limit
+            command:
+              - "/bin/bash"
+              - "-c"
+            args:
+              - "/galaxy/server/scripts/maintenance.sh"
+              - "--no-dry-run"
+              - "--days"
+              - {{ .Values.maintenance.script.days | quote }}
+            volumeMounts:
+            - name: galaxy-data
+              mountPath: {{ .Values.persistence.mountPath }}
+          volumes:
+          - name: galaxy-data
+            {{- if .Values.persistence.enabled }}
+            persistentVolumeClaim:
+              claimName: {{ template "galaxy.pvcname" . }}
+            {{- else }}
+            emptyDir: {}
+            {{- end }}
+          restartPolicy: OnFailure
+{{- end }}
+{{ if .Values.cronJobs -}}
+{{ range $key, $cronjob := .Values.cronJobs }}
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "galaxy.fullname" $ }}-maintenance-{{ $key }}
+  labels:
+    {{- include "galaxy.labels" $ | nindent 4 }}
+spec:
+  schedule: {{ $cronjob.schedule | quote }}
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          {{- if $cronjob.securityContext }}
+          securityContext:
+            {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- end}}
+          {{- with $.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 16 }}
+          {{- end }}
+          containers:
+          - name: galaxy-maintenance-{{ $key }}
+            image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
+            imagePullPolicy: {{ $.Values.image.pullPolicy }}
+            # delete all tmp files older than walltime limit
+            command:
+            {{- range $cmd := $cronjob.command }}
+              - {{ tpl $cmd $ | quote }}
+            {{- end}}
+            {{- if $cronjob.args }}
+            args:
+              {{- range $arg := $cronjob.args }}
+              - {{ tpl $arg $ | quote }}
+              {{- end }}
+            {{- end }}
+            volumeMounts:
+            - name: galaxy-data
+              mountPath: {{ $.Values.persistence.mountPath }}
+          volumes:
+          - name: galaxy-data
+            {{- if $.Values.persistence.enabled }}
+            persistentVolumeClaim:
+              claimName: {{ template "galaxy.pvcname" $ }}
+            {{- else }}
+            emptyDir: {}
+            {{- end }}
+          restartPolicy: OnFailure
+{{- end }}
+{{- end }}

galaxy/templates/hook-cvmfs-fix.yaml

@@ -1,5 +1,5 @@
 {{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
-  # Include the code you want to run when both conditions are met
+# Include the code you want to run when both conditions are met
 apiVersion: batch/v1
 kind: Job
 metadata:

galaxy/values.yaml

@@ -267,6 +267,31 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+#- User defined CronJobs
+cronJobs:
+  chown:
+    schedule: "0 * * * *"
+    securityContext:
+      runAsUser: 0
+    command:
+      - /usr/bin/chown
+    args:
+      - "-R"
+      - "galaxy"
+      - "/galaxy/server/database"
+#- Maintenance tasks that should be run periodically to prevent storage from being exhausted
+maintenance:
+  #- Remove files in the tmp directory.
+  tmp:
+    enabled: true
+    schedule: "5 2 * * *"
+    seconds: "604800" # Default wall time for jobs
+  #- The maintenance script removes histories, datasets, and other Galaxy objects older than 7 days.
+  script:
+    enabled: true
+    schedule: "10 2 * * *"
+    days: "7"
+
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true