A Helm chart for deploying the Seqr app, an open source software platform for rare disease genomics
Homepage: https://seqr.broadinstitute.org
| Name | Url | |
|---|---|---|
| seqr | seqr@broadinstitute.org |
| Repository | Name | Version |
|---|---|---|
| file://../lib | lib | 1.1.0 |
| https://charts.bitnami.com/bitnami | clickhouse | 9.2.2 |
| https://charts.bitnami.com/bitnami | postgresql | 15.5.31 |
| https://charts.bitnami.com/bitnami | redis | 19.0.2 |
| Key | Type | Default | Description |
|---|---|---|---|
| additionalSecrets | object | {} |
|
| 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\"" |
|
| clickhouse.additionalConfigdFiles | object | {} |
|
| clickhouse.additionalSidecars | object | {} |
|
| clickhouse.additionalUsersdFiles | object | {} |
|
| clickhouse.auth.existingSecret | string | "clickhouse-secrets" |
|
| clickhouse.auth.existingSecretKey | string | "admin_password" |
|
| clickhouse.auth.username | string | "seqr_clickhouse_admin" |
|
| clickhouse.enabled | bool | false |
|
| clickhouse.existingConfigdConfigmap | string | "seqr-clickhouse-configd-config" |
|
| clickhouse.existingUsersdConfigmap | string | "seqr-clickhouse-usersd-config" |
|
| clickhouse.extraEnvVars[0].name | string | "POSTGRES_PASSWORD" |
|
| clickhouse.extraEnvVars[0].valueFrom.secretKeyRef.key | string | "password" |
|
| clickhouse.extraEnvVars[0].valueFrom.secretKeyRef.name | string | "postgres-secrets" |
|
| clickhouse.extraEnvVars[1].name | string | "CLICKHOUSE_READER_PASSWORD" |
|
| clickhouse.extraEnvVars[1].valueFrom.secretKeyRef.key | string | "reader_password" |
|
| clickhouse.extraEnvVars[1].valueFrom.secretKeyRef.name | string | "clickhouse-secrets" |
|
| clickhouse.extraEnvVars[2].name | string | "CLICKHOUSE_WRITER_PASSWORD" |
|
| clickhouse.extraEnvVars[2].valueFrom.secretKeyRef.key | string | "writer_password" |
|
| clickhouse.extraEnvVars[2].valueFrom.secretKeyRef.name | string | "clickhouse-secrets" |
|
| clickhouse.extraEnvVars[3].name | string | "CLICKHOUSE_VLM_PASSWORD" |
|
| clickhouse.extraEnvVars[3].valueFrom.secretKeyRef.key | string | "seqr_clickhouse_vlm_password" |
|
| clickhouse.extraEnvVars[3].valueFrom.secretKeyRef.name | string | "vlm-secrets" |
|
| clickhouse.extraEnvVars[3].valueFrom.secretKeyRef.optional | bool | true |
|
| clickhouse.extraEnvVars[4].name | string | "PIPELINE_DATA_DIR_HMAC_KEY" |
|
| clickhouse.extraEnvVars[4].valueFrom.secretKeyRef.key | string | "pipeline_data_dir_hmac_key" |
|
| clickhouse.extraEnvVars[4].valueFrom.secretKeyRef.name | string | "clickhouse-hmac-secrets" |
|
| clickhouse.extraEnvVars[4].valueFrom.secretKeyRef.optional | bool | true |
|
| clickhouse.extraEnvVars[5].name | string | "PIPELINE_DATA_DIR_HMAC_SECRET" |
|
| clickhouse.extraEnvVars[5].valueFrom.secretKeyRef.key | string | "pipeline_data_dir_hmac_secret" |
|
| clickhouse.extraEnvVars[5].valueFrom.secretKeyRef.name | string | "clickhouse-hmac-secrets" |
|
| clickhouse.extraEnvVars[5].valueFrom.secretKeyRef.optional | bool | true |
|
| clickhouse.extraVolumeMounts[0].mountPath | string | "/in-memory-dir" |
|
| clickhouse.extraVolumeMounts[0].name | string | "in-memory-dir" |
|
| clickhouse.extraVolumeMounts[1].mountPath | string | "/bitnami/clickhouse/data" |
|
| clickhouse.extraVolumeMounts[1].name | string | "empty-dir" |
|
| clickhouse.extraVolumeMounts[1].subPath | string | "app-volume-dir-for-init" |
|
| clickhouse.extraVolumes[0].emptyDir.medium | string | "Memory" |
|
| clickhouse.extraVolumes[0].name | string | "in-memory-dir" |
|
| clickhouse.fullnameOverride | string | "seqr-clickhouse" |
|
| clickhouse.image.repository | string | "bitnamilegacy/clickhouse" |
|
| clickhouse.image.tag | string | "25.4.3" |
|
| clickhouse.initContainers[0].command[0] | string | "/bin/sh" |
|
| clickhouse.initContainers[0].command[1] | string | "-ec" |
|
| clickhouse.initContainers[0].command[2] | string | "mkdir -p {{ .Values.global.seqr.environment.CLICKHOUSE_DATA_DIR }}\nchown -R 1001:1001 {{ .Values.global.seqr.environment.CLICKHOUSE_DATA_DIR }}\n" |
|
| clickhouse.initContainers[0].image | string | "busybox" |
|
| clickhouse.initContainers[0].name | string | "seqr-clickhouse-init-chmod-data" |
|
| clickhouse.initContainers[0].securityContext.runAsGroup | int | 1001 |
|
| clickhouse.initContainers[0].securityContext.runAsNonRoot | bool | false |
|
| clickhouse.initContainers[0].securityContext.seLinuxOptions | object | {} |
|
| clickhouse.initContainers[0].securityContext.seccompProfile.type | string | "RuntimeDefault" |
|
| clickhouse.initContainers[0].volumeMounts[0].mountPath | string | "{{ .Values.persistence.mountPath }}" |
|
| clickhouse.initContainers[0].volumeMounts[0].name | string | "data" |
|
| clickhouse.initContainers[1].command[0] | string | "/bin/sh" |
|
| clickhouse.initContainers[1].command[1] | string | "-c" |
|
| clickhouse.initContainers[1].command[2] | string | "mkdir -p $CLICKHOUSE_DATA_DIR \u0026\u0026 cd $CLICKHOUSE_DATA_DIR \u0026\u0026 find . -type f | grep -E \"GRCh(37|38)/[^/]+/(v[0-9]+/)?annotations\" | xargs -I{} -P16 cp -v --parents {} $CLICKHOUSE_IN_MEMORY_DIR \u0026\u0026 chown -R 1001:1001 $CLICKHOUSE_IN_MEMORY_DIR" |
|
| clickhouse.initContainers[1].env[0].name | string | "CLICKHOUSE_IN_MEMORY_DIR" |
|
| clickhouse.initContainers[1].env[0].value | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_IN_MEMORY_DIR }}" |
|
| clickhouse.initContainers[1].env[1].name | string | "CLICKHOUSE_DATA_DIR" |
|
| clickhouse.initContainers[1].env[1].value | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_DATA_DIR }}" |
|
| clickhouse.initContainers[1].image | string | "busybox" |
|
| clickhouse.initContainers[1].name | string | "sync-annotations-disk" |
|
| clickhouse.initContainers[1].volumeMounts[0].mountPath | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_IN_MEMORY_DIR }}" |
|
| clickhouse.initContainers[1].volumeMounts[0].name | string | "in-memory-dir" |
|
| clickhouse.initContainers[1].volumeMounts[1].mountPath | string | "{{ .Values.persistence.mountPath }}" |
|
| clickhouse.initContainers[1].volumeMounts[1].name | string | "data" |
|
| clickhouse.initContainers[2].command[0] | string | "/bin/sh" |
|
| clickhouse.initContainers[2].command[1] | string | "-c" |
|
| clickhouse.initContainers[2].command[2] | string | "mkdir -p $CLICKHOUSE_DATA_DIR \u0026\u0026 cd $CLICKHOUSE_DATA_DIR \u0026\u0026 find . -type f | grep -E \"GRCh(37|38)/[^/]+/(v[0-9]+/)?variants\" | grep -v \"/variants_details\" | xargs -I{} -P16 cp -v --parents {} $CLICKHOUSE_IN_MEMORY_DIR \u0026\u0026 chown -R 1001:1001 $CLICKHOUSE_IN_MEMORY_DIR" |
|
| clickhouse.initContainers[2].env[0].name | string | "CLICKHOUSE_IN_MEMORY_DIR" |
|
| clickhouse.initContainers[2].env[0].value | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_IN_MEMORY_DIR }}" |
|
| clickhouse.initContainers[2].env[1].name | string | "CLICKHOUSE_DATA_DIR" |
|
| clickhouse.initContainers[2].env[1].value | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_DATA_DIR }}" |
|
| clickhouse.initContainers[2].image | string | "busybox" |
|
| clickhouse.initContainers[2].name | string | "sync-variants-disk" |
|
| clickhouse.initContainers[2].volumeMounts[0].mountPath | string | "{{ .Values.global.seqr.environment.CLICKHOUSE_IN_MEMORY_DIR }}" |
|
| clickhouse.initContainers[2].volumeMounts[0].name | string | "in-memory-dir" |
|
| clickhouse.initContainers[2].volumeMounts[1].mountPath | string | "{{ .Values.persistence.mountPath }}" |
|
| clickhouse.initContainers[2].volumeMounts[1].name | string | "data" |
|
| clickhouse.initdbScriptsSecret | string | "seqr-clickhouse-init-db-secret" |
|
| clickhouse.initdbSecretEnabled | bool | true |
|
| clickhouse.keeper.enabled | bool | false |
|
| clickhouse.networkPolicy.enabled | bool | false |
|
| clickhouse.persistence.enabled | bool | true |
|
| clickhouse.persistence.existingClaim | string | "{{ include \"lib.pvc-name\" . }}" |
|
| clickhouse.persistence.mountPath | string | "/var/seqr" |
|
| clickhouse.replicaCount | int | 1 |
|
| clickhouse.resourcesPreset | string | "none" |
|
| clickhouse.serviceAccount.create | bool | true |
|
| clickhouse.serviceAccount.name | string | "seqr-clickhouse" |
|
| clickhouse.shards | int | 1 |
|
| clickhouse.sidecars | string | "{{- with .Values.additionalSidecars }}\n {{- tpl . $ | nindent 0}}\n{{- end }}" |
|
| clickhouse.usePasswordFiles | bool | false |
|
| cronJobs[0].command | string | "python manage.py check_for_new_samples_from_pipeline" |
|
| cronJobs[0].name | string | "check-new-samples-job" |
|
| cronJobs[0].schedule | string | "*/10 * * * *" |
|
| cronJobs[1].command | string | "python manage.py update_all_reference_data" |
|
| cronJobs[1].name | string | "update-all-reference-data" |
|
| cronJobs[1].schedule | string | "*/5 * * * *" |
|
| cronJobs[2].command | string | "python /seqr/manage.py check; python /seqr/manage.py reload_clinvar_all_variants" |
|
| cronJobs[2].name | string | "reload-clinvar-all-variants" |
|
| cronJobs[2].schedule | string | "30 0 * * *" |
|
| cronJobs[2].timeout_s | int | 7200 |
|
| cronJobs[3].command | string | "python manage.py register_caids" |
|
| cronJobs[3].name | string | "register-caids" |
|
| cronJobs[3].schedule | string | "0,30 * * * *" |
|
| deploymentAnnotations | object | {} |
|
| environment.CLICKHOUSE_READER_USER | string | "seqr_clickhouse_reader" |
|
| environment.CLICKHOUSE_VLM_USERNAME | string | "vlm_clickhouse_reader" |
|
| environment.CLICKHOUSE_WRITER_USER | string | "seqr_clickhouse_writer" |
|
| environment.GUNICORN_WORKER_THREADS | string | "4" |
The number of threads to allocate to the gunicorn server |
| environment.HGMD_GRCH37_URL | string | null |
|
| environment.HGMD_GRCH38_URL | string | null |
|
| environment.LUIGI_UI_SERVICE_HOSTNAME | string | "pipeline-runner-ui" |
|
| environment.LUIGI_UI_SERVICE_PORT | string | "8082" |
|
| environment.PIPELINE_RUNNER_HOSTNAME | string | "pipeline-runner-api" |
|
| environment.PIPELINE_RUNNER_PORT | string | "6000" |
|
| environment.POSTGRES_SERVICE_HOSTNAME | string | "seqr-postgresql" |
The hostname to use for the postgres database connectsion |
| environment.POSTGRES_SERVICE_PORT | string | "5432" |
The TCP port number to use for the postgres database connection |
| environment.POSTGRES_USERNAME | string | "postgres" |
The username to use for the postgres database connection |
| environment.REDIS_SERVICE_HOSTNAME | string | "seqr-redis-master" |
The hostname of the redis cache that seqr should use |
| environment.REDIS_SERVICE_PORT | string | "6379" |
The port of the redis cache that seqr should use |
| environment.SEQR_SERVICE_PORT | string | "8000" |
The port that the seqr server should listen on |
| environment.STATIC_MEDIA_DIR | string | "/var/seqr/seqr-static-media" |
If storing static media files in a local filesystem, the path to that filesystem |
| global.security.allowInsecureImages | bool | true |
|
| global.seqr.environment.CLICKHOUSE_DATA_DIR | string | "/var/seqr/clickhouse-data" |
|
| global.seqr.environment.CLICKHOUSE_IN_MEMORY_DIR | string | "/in-memory-dir" |
|
| global.seqr.environment.CLICKHOUSE_LOADER_DISABLED | string | "0" |
|
| global.seqr.environment.CLICKHOUSE_SERVICE_HOSTNAME | string | "seqr-clickhouse" |
|
| global.seqr.environment.LOADING_DATASETS_DIR | string | "/var/seqr/seqr-loading-temp" |
|
| global.seqr.environment.PIPELINE_DATA_DIR | string | "/var/seqr/pipeline-data" |
|
| global.seqrPlatformDeploy | bool | false |
|
| image.pullPolicy | string | "Always" |
|
| image.repository | string | "gcr.io/seqr-project/seqr" |
|
| imagePullSecrets | list | [] |
|
| ingress.enabled | bool | false |
|
| initContainers | string | "{{- if not (hasPrefix \"gs://\" $.Values.global.seqr.environment.LOADING_DATASETS_DIR) }}\n- name: mkdir-loading-datasets\n image: busybox:1.35\n imagePullPolicy: {{ $.Values.image.pullPolicy }}\n command: ['/bin/mkdir', '-p', {{ $.Values.global.seqr.environment.LOADING_DATASETS_DIR }}]\n {{- with $.Values.volumeMounts }}\n volumeMounts:\n {{- tpl . $ | nindent 4 }}\n {{- end }}\n{{- else }}\n []\n{{- end }}" |
|
| jobAfterHook | string | "" |
|
| jobBeforeHook | string | "" |
|
| networkPolicy.enabled | bool | false |
|
| nodeSelector | object | {} |
|
| podAnnotations | object | {} |
|
| postgresql.architecture | string | "standalone" |
|
| postgresql.auth.existingSecret | string | "postgres-secrets" |
|
| postgresql.auth.secretKeys.adminPasswordKey | string | "password" |
|
| postgresql.auth.username | string | "postgres" |
|
| postgresql.enabled | bool | true |
Set to "false" to disable the postgresql deployent (if you're using a managed cloud database). |
| postgresql.fullnameOverride | string | "seqr-postgresql" |
|
| postgresql.image.repository | string | "bitnamilegacy/postgresql" |
|
| postgresql.image.tag | string | "12.19.0-debian-12-r9" |
|
| postgresql.postgresqlDataDir | string | "/var/seqr/postgresql-data" |
|
| postgresql.primary.initContainers[0].command[0] | string | "/bin/sh" |
|
| postgresql.primary.initContainers[0].command[1] | string | "-ec" |
|
| postgresql.primary.initContainers[0].command[2] | string | "mkdir -p {{ .Values.postgresqlDataDir }}\nchown -R `id -u`:`id -G | cut -d \" \" -f2` {{ .Values.postgresqlDataDir }}\n" |
|
| postgresql.primary.initContainers[0].image | string | "bitnamilegacy/os-shell" |
|
| postgresql.primary.initContainers[0].imagePullPolicy | string | "IfNotPresent" |
|
| postgresql.primary.initContainers[0].name | string | "seqr-postgresql-init-chmod-data" |
|
| postgresql.primary.initContainers[0].securityContext.runAsGroup | int | 1001 |
|
| postgresql.primary.initContainers[0].securityContext.runAsNonRoot | bool | false |
|
| postgresql.primary.initContainers[0].securityContext.seLinuxOptions | object | {} |
|
| postgresql.primary.initContainers[0].securityContext.seccompProfile.type | string | "RuntimeDefault" |
|
| postgresql.primary.initContainers[0].volumeMounts[0].mountPath | string | "/var/seqr" |
|
| postgresql.primary.initContainers[0].volumeMounts[0].name | string | "data" |
|
| postgresql.primary.initdb.scripts."00_init.sql" | string | "CREATE DATABASE seqrdb;\nCREATE DATABASE reference_data_db;\n" |
|
| postgresql.primary.persistence.existingClaim | string | "{{ include \"lib.pvc-name\" . }}" |
|
| postgresql.primary.persistence.mountPath | string | "/var/seqr" |
|
| postgresql.primary.resources.limits.memory | string | "2Gi" |
|
| postgresql.primary.startupProbe.enabled | bool | true |
|
| redis.architecture | string | "standalone" |
|
| redis.auth.enabled | bool | false |
|
| redis.enabled | bool | true |
Set to "false" to disable the redis cache (if you're using a managed cache service). |
| redis.fullnameOverride | string | "seqr-redis" |
|
| redis.image.repository | string | "bitnamilegacy/redis" |
|
| redis.networkPolicy.enabled | bool | false |
|
| replicaCount | int | 1 |
|
| requiredSecrets | object | {
"clickhouseSecretName": "clickhouse-secrets",
"postgresSecretName": "postgres-secrets",
"seqrSecretName": "seqr-secrets"
} |
Secrets which are required for seqr's functionality |
| requiredSecrets.postgresSecretName | string | "postgres-secrets" |
The secret containing the postgres credentials. See the README for information on the format of this secret |
| requiredSecrets.seqrSecretName | string | "seqr-secrets" |
The secret containing the seqr required secrets. See the README for information on the format of this secret |
| resources | object | {} |
|
| service.nodePort | int | 30950 |
|
| service.port | int | 8000 |
|
| service.type | string | "NodePort" |
|
| serviceAccount.annotations | object | {} |
|
| serviceAccount.create | bool | true |
|
| tolerations | list | [] |
|
| updateAllReferenceDataPostInstallJob.enabled | bool | true |
|
| volumeMounts | string | "- name: seqr-datasets\n mountPath: /var/seqr\n readOnly: false" |
|
| volumes | string | "- name: seqr-datasets\n persistentVolumeClaim:\n readOnly: false\n claimName: {{ include \"lib.pvc-name\" . }}" |
Autogenerated from chart metadata using helm-docs v1.14.2