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pipeline-runner

Version: 2.160.0 Type: application AppVersion: 662a3a1fb5f9bcb3e5a5aa29067951843eff0a6e

A Helm chart for deploying the loading pipeline of Seqr, an open source software platform for rare disease genomics

Maintainers

Name Email Url
seqr seqr@broadinstitute.org

Source Code

Requirements

Repository Name Version
file://../lib lib 1.1.0

Values

Key Type Default Description
additionalSecrets[0].name string 
"CLICKHOUSE_WRITER_PASSWORD"
additionalSecrets[0].valueFrom.secretKeyRef.key string 
"writer_password"
additionalSecrets[0].valueFrom.secretKeyRef.name string 
"clickhouse-secrets"
affinity string 
"podAntiAffinity:\n  preferredDuringSchedulingIgnoredDuringExecution:\n    - weight: 1.0\n      podAffinityTerm:\n        labelSelector:\n          matchExpressions:\n            - key: \"app.kubernetes.io/part-of\"\n              operator: In\n              values:\n              - \"seqr-platform\"\n        topologyKey: \"kubernetes.io/hostname\""
cronJobs[0].command string 
"./loading_pipeline/bin/rsync_reference_data.bash GRCh37 \u0026\u0026 ./loading_pipeline/bin/download_vep_reference_data.bash GRCh37"
cronJobs[0].name string 
"reference-data-sync-37"
cronJobs[0].schedule string 
"*/5 * * * *"
cronJobs[1].command string 
"./loading_pipeline/bin/rsync_reference_data.bash GRCh38 \u0026\u0026 ./loading_pipeline/bin/download_vep_reference_data.bash GRCh38"
cronJobs[1].name string 
"reference-data-sync-38"
cronJobs[1].schedule string 
"*/5 * * * *"
deploymentAnnotations object 
{}
environment.CLICKHOUSE_WRITER_USER string 
"seqr_clickhouse_writer"
environment.LUIGI_STATE_DIR string 
"/var/seqr/luigi-state"
environment.PIPELINE_DATA_DIR string 
"/var/seqr/pipeline-data"
environment.REFERENCE_DATASETS_DIR string 
"/var/seqr/seqr-reference-data"
global.seqr.environment.CLICKHOUSE_SERVICE_HOSTNAME string 
"seqr-clickhouse"
global.seqrPlatformDeploy bool 
false
hailWorkerResources string 
"requests:\n  memory: \"12Gi\""
image.pullPolicy string 
"Always"
image.repository string 
"gcr.io/seqr-project/seqr-pipeline-runner"
imagePullSecrets list 
[]
jobAfterHook string 
""
jobBeforeHook string 
""
networkPolicy.enabled bool 
false
nodeSelector object 
{}
podAnnotations object 
{}
pods[0].command[0] string 
"uv"
pods[0].command[1] string 
"run"
pods[0].command[2] string 
"python3"
pods[0].command[3] string 
"-m"
pods[0].command[4] string 
"loading_pipeline.api"
pods[0].healthCheckRoute string 
"/status"
pods[0].initContainers object 
{}
pods[0].name string 
"api"
pods[0].resources object 
{}
pods[0].service.port int 
6000
pods[0].service.type string 
"ClusterIP"
pods[0].sidecar.command[0] string 
"uv"
pods[0].sidecar.command[1] string 
"run"
pods[0].sidecar.command[2] string 
"python3"
pods[0].sidecar.command[3] string 
"-m"
pods[0].sidecar.command[4] string 
"loading_pipeline.bin.pipeline_worker"
pods[0].sidecar.privileged bool 
true
pods[1].command[0] string 
"uv"
pods[1].command[1] string 
"run"
pods[1].command[2] string 
"luigid"
pods[1].healthCheckRoute string 
"/"
pods[1].initContainers string 
"- name: mkdir-luigi-state\n  image: busybox:1.35\n  imagePullPolicy: {{ .Values.image.pullPolicy }}\n  command: ['/bin/mkdir', '-p', {{ .Values.environment.LUIGI_STATE_DIR }}]\n  {{- with $.Values.volumeMounts }}\n  volumeMounts:\n    {{- tpl . $ | nindent 4 }}\n  {{- end }}"
pods[1].name string 
"ui"
pods[1].resources object 
{}
pods[1].service.nodePort int 
30951
pods[1].service.port int 
8082
pods[1].service.type string 
"NodePort"
pods[1].sidecar object 
{}
serviceAccount.annotations object 
{}
serviceAccount.create bool 
true
tolerations list 
[]
volumeMounts string 
"- name: seqr-datasets\n  mountPath: /var/seqr\n  readOnly: false\n- name: docker-socket\n  mountPath: /var/run/docker.sock\n  readOnly: false\n- name: luigi-config\n  mountPath: /etc/luigi/luigi.cfg\n  subPath: luigi.cfg"
volumes string 
"- name: seqr-datasets\n  persistentVolumeClaim:\n    readOnly: false\n    claimName: {{ include \"lib.pvc-name\" . }}\n- name: docker-socket\n  hostPath:\n    path: /var/run/docker.sock\n- name: luigi-config\n  configMap:\n    name: luigi-config\n    items:\n      - key: luigi.cfg\n        path: luigi.cfg"

Autogenerated from chart metadata using helm-docs v1.14.2