seqr-helm/charts/pipeline-runner/values.yaml at main · broadinstitute/seqr-helm · GitHub

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image:
  repository: gcr.io/seqr-project/seqr-pipeline-runner
  pullPolicy: Always
imagePullSecrets: []

serviceAccount:
  create: true
  annotations: {}

podAnnotations: {}
deploymentAnnotations: {}

additionalSecrets:
  - name: CLICKHOUSE_WRITER_PASSWORD
    valueFrom:
      secretKeyRef:
        name: clickhouse-secrets
        key: writer_password

volumes: |-
  - name: seqr-datasets
    persistentVolumeClaim:
      readOnly: false
      claimName: {{ include "lib.pvc-name" . }}
  - name: docker-socket
    hostPath:
      path: /var/run/docker.sock
  - name: luigi-config
    configMap:
      name: luigi-config
      items:
        - key: luigi.cfg
          path: luigi.cfg
volumeMounts: |-
  - name: seqr-datasets
    mountPath: /var/seqr
    readOnly: false
  - name: docker-socket
    mountPath: /var/run/docker.sock
    readOnly: false
  - name: luigi-config
    mountPath: /etc/luigi/luigi.cfg
    subPath: luigi.cfg

pods:
  - name: api
    service:
      type: ClusterIP
      port: 6000
    healthCheckRoute: /status
    command: ["uv", "run", "python3", "-m", "loading_pipeline.api"]
    initContainers: {}
    resources: {}
    sidecar:
      command: ["uv", "run", "python3", "-m", "loading_pipeline.bin.pipeline_worker"]
      privileged: true
  - name: ui
    service:
      type: NodePort
      port: 8082
      nodePort: 30951
    healthCheckRoute: /
    command: ["uv", "run", "luigid"]
    initContainers: |-
      - name: mkdir-luigi-state
        image: busybox:1.35
        imagePullPolicy: {{ .Values.image.pullPolicy }}
        command: ['/bin/mkdir', '-p', {{ .Values.environment.LUIGI_STATE_DIR }}]
        {{- with $.Values.volumeMounts }}
        volumeMounts:
          {{- tpl . $ | nindent 4 }}
        {{- end }}
    resources: {}
    sidecar: {}

networkPolicy:
  enabled: false
hailWorkerResources: |-
  requests:
    memory: "12Gi"
environment:
  REFERENCE_DATASETS_DIR: "/var/seqr/seqr-reference-data"
  PIPELINE_DATA_DIR: "/var/seqr/pipeline-data"
  LUIGI_STATE_DIR: "/var/seqr/luigi-state"
  CLICKHOUSE_WRITER_USER: "seqr_clickhouse_writer"

affinity: |-
  podAntiAffinity:
    preferredDuringSchedulingIgnoredDuringExecution:
      - weight: 1.0
        podAffinityTerm:
          labelSelector:
            matchExpressions:
              - key: "app.kubernetes.io/part-of"
                operator: In
                values:
                - "seqr-platform"
          topologyKey: "kubernetes.io/hostname"
nodeSelector: {}
tolerations: []

jobAfterHook: ""
jobBeforeHook: ""
cronJobs:
  - name: reference-data-sync-37
    schedule: "*/5 * * * *"
    command: "./loading_pipeline/bin/rsync_reference_data.bash GRCh37 && ./loading_pipeline/bin/download_vep_reference_data.bash GRCh37"
  - name: reference-data-sync-38
    schedule: "*/5 * * * *"
    command: "./loading_pipeline/bin/rsync_reference_data.bash GRCh38 && ./loading_pipeline/bin/download_vep_reference_data.bash GRCh38"

global:
  seqrPlatformDeploy: false
  seqr:
    environment:
      CLICKHOUSE_SERVICE_HOSTNAME: 'seqr-clickhouse'