pipeline-runner

pipeline-runner

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

• https://github.com/broadinstitute/seqr-helm
• https://github.com/broadinstitute/seqr-loading-pipelines

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"

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Autogenerated from chart metadata using helm-docs v1.14.2