chore(opal): removed from third-party repo
This commit is contained in:
parent
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@ -1,6 +1,6 @@
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# Third party - Helm templates
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These are the Helm templates that we will use for MOLGENIS operations.
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These are the Helm templates that we will use for third-party operations.
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## Kubernetes
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When you want to use kubernetes there are some commands you need to know. Also running on a remote cluster will be a must have to control your whole DTAP.
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apiVersion: v1
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appVersion: "1.0"
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description: Opal - helm stack (in BETA)
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name: opal
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version: 0.0.1
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sources:
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- https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm.git
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icon: https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm/
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home: https://obiba.org
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maintainers:
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- name: sidohaakma
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- name: fdlk
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# Opal
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This chart is used for acceptance and production use cases.
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## Containers
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The created containers are:
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- Opal
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- MongoDB
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- RServer
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## Provisioning
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You can choose from which registry you want to pull. There is 1 one registry:
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- https://hub.docker.com
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categories:
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- OPAL
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questions:
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- variable: opal.environment
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label: Environment
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default: "test"
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description: "Environment of Opal instance"
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type: enum
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options:
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- development
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- test
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- acceptance
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- production
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required: true
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group: "Provisioning"
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- variable: molgenis.type.kind
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label: Type
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default: "medium"
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description: "Type of MOLGENIS resources"
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type: enum
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options:
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- small
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- medium
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- large
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required: true
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group: "Provisioning"
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- variable: molgenis.image.tag
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label: Version
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default: "stable"
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description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
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type: string
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required: true
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group: "Provisioning"
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@ -1,6 +0,0 @@
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dependencies:
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- name: mysql
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repository: https://kubernetes-charts.storage.googleapis.com/
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version: 0.10.2
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digest: sha256:77710fe100fb005d51e006d2e19643f9af2b1aadd1c2249c67ffc5be6a095f30
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generated: 2018-11-06T15:57:20.530933765Z
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@ -1,4 +0,0 @@
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dependencies:
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- name: mysql
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version: ^0.10.2
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repository: https://kubernetes-charts.storage.googleapis.com/
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1. Get the application URL by running these commands:
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{{- if .Values.ingress.enabled }}
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{{- range .Values.ingress.hosts }}
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http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
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{{- end }}
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{{- else if contains "NodePort" .Values.service.type }}
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export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
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export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
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echo http://$NODE_IP:$NODE_PORT
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{{- else if contains "LoadBalancer" .Values.service.type }}
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NOTE: It may take a few minutes for the LoadBalancer IP to be available.
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You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
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export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
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echo http://$SERVICE_IP:{{ .Values.service.port }}
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{{- else if contains "ClusterIP" .Values.service.type }}
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
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echo "Visit http://127.0.0.1:8080 to use your application"
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kubectl port-forward $POD_NAME 8080:80
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{{- end }}
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{{/* vim: set filetype=mustache: */}}
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{{/*
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Expand the name of the chart.
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*/}}
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{{- define "opal.name" -}}
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{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
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{{- end -}}
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{{/*
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Create a default fully qualified app name.
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We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
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If release name contains chart name it will be used as a full name.
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*/}}
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{{- define "opal.fullname" -}}
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{{- if .Values.fullnameOverride -}}
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{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
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{{- else -}}
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{{- $name := default .Chart.Name .Values.nameOverride -}}
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{{- if contains $name .Release.Name -}}
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{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
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{{- else -}}
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{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
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{{- end -}}
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{{- end -}}
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{{- end -}}
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{{/*
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Create chart name and version as used by the chart label.
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*/}}
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{{- define "opal.chart" -}}
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{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
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{{- end -}}
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apiVersion: apps/v1beta2
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kind: Deployment
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metadata:
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{{- with .Values.ingress.annotations }}
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annotations:
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{{ toYaml . | indent 4 }}
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{{- end }}
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name: {{ template "opal.fullname" . }}
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labels:
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app: {{ template "opal.name" . }}
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chart: {{ template "opal.chart" . }}
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release: {{ .Release.Name }}
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heritage: {{ .Release.Service }}
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spec:
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replicas: {{ .Values.replicaCount }}
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selector:
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matchLabels:
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app: {{ template "opal.name" . }}
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release: {{ .Release.Name }}
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strategy:
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type: Recreate
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template:
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metadata:
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labels:
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app: {{ template "opal.name" . }}
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release: {{ .Release.Name }}
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spec:
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containers:
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- name: opal
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{{- with .Values.opal }}
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image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
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imagePullPolicy: {{ .image.pullPolicy }}
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env:
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- name: OPAL_ADMINISTRATOR_PASSWORD
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value: "{{ .adminPassword }}"
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ports:
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- containerPort: {{ $.Values.service.port }}
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{{- if $.Values.persistence.enabled }}
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volumeMounts:
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- name: opal-nfs
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mountPath: /home/opal
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{{- end }}
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livenessProbe:
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httpGet:
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path: /
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port: {{ $.Values.service.port }}
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initialDelaySeconds: 60
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periodSeconds: 5
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failureThreshold: 25
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successThreshold: 1
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resources:
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{{ toYaml .resources | indent 12 }}
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{{- end }}
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- name: rserver
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{{- with .Values.rserver }}
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image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
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imagePullPolicy: {{ .image.pullPolicy }}
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ports:
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- containerPort: 6612
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- containerPort: 6311
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resources:
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{{ toYaml .resources | indent 12 }}
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{{- end }}
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{{- if .Values.persistence.enabled }}
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volumes:
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- name: opal-nfs
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persistentVolumeClaim:
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claimName: {{ .Release.Name }}-{{ .Values.opal.persistence.claim }}
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{{- end }}
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{{- with .Values.nodeSelector }}
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nodeSelector:
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{{ toYaml . | indent 8 }}
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{{- end }}
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{{- with .Values.affinity }}
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affinity:
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{{ toYaml . | indent 8 }}
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{{- end }}
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{{- with .Values.tolerations }}
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tolerations:
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{{ toYaml . | indent 8 }}
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{{- end }}
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{{- if .Values.ingress.enabled -}}
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{{- $fullName := include "opal.fullname" . -}}
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{{- $ingressPath := .Values.ingress.path -}}
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apiVersion: extensions/v1beta1
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kind: Ingress
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metadata:
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name: "{{ $.Release.Name }}-ingress"
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labels:
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app: {{ $.Values.service.name }}
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chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
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release: "{{ .Release.Name }}"
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heritage: "{{ .Release.Service }}"
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{{- with .Values.ingress.annotations }}
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annotations:
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{{ toYaml . | indent 4 }}
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{{- end }}
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spec:
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{{- if .Values.ingress.tls }}
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tls:
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{{- range .Values.ingress.tls }}
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- hosts:
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{{- range .hosts }}
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- {{ . }}
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{{- end }}
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secretName: {{ .secretName }}
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{{- end }}
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{{- end }}
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rules:
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{{- if .Values.ingress.hosts }}
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{{- range $host := .Values.ingress.hosts }}
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- host: {{ $host }}
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http:
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paths:
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- path: {{ $ingressPath }}
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backend:
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serviceName: {{ $.Values.service.name }}
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servicePort: {{ $.Values.service.port }}
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{{- end }}
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{{- end }}
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{{- end }}
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{{- if .Values.persistence.enabled -}}
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apiVersion: extensions/v1beta1
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kind: PersistentVolumeClaim
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apiVersion: v1
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metadata:
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name: {{ .Release.Name }}-{{ .Values.opal.persistence.claim }}
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annotations:
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{{- if .Values.persistence.retain }}
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volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
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{{- else }}
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volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
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{{- end }}
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spec:
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accessModes:
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- ReadWriteMany
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resources:
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requests:
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storage: {{ .Values.opal.persistence.size }}
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{{- end }}
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apiVersion: v1
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kind: Service
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metadata:
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name: "{{ .Release.Name }}-{{ .Values.service.name }}"
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labels:
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app: "{{ .Release.Name }}-{{ .Values.service.name }}"
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chart: {{ template "opal.chart" . }}
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release: {{ .Release.Name }}
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heritage: {{ .Release.Service }}
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spec:
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type: {{ .Values.service.type }}
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ports:
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- name: "{{ .Release.Name }}-{{ .Values.service.name }}"
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port: {{ .Values.service.port }}
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selector:
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app: {{ template "opal.name" . }}
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release: {{ .Release.Name }}
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# Default values for molgenis.
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replicaCount: 1
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service:
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name: opal
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type: ClusterIP
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port: 8080
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ingress:
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enabled: true
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annotations:
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nginx.ingress.kubernetes.io/proxy-body-size: "0"
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hosts:
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- opal.dev.molgenis.org
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path: /
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tls: []
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opal:
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advanced: false
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javaOpts:
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maxHeapSpace: "4g"
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resources:
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limits:
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cpu: 1
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memory: 2Gi
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requests:
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cpu: 200m
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memory: 4Gi
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persistence:
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size: 10Gi
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image:
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repository: registry.hub.docker.com
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name: obiba/opal
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tag: latest
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pullPolicy: Always
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adminPassword: ?01LifeCycle!
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persistence:
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claim: pvc-opal
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size: 10Gi
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containerPorts:
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- 8080
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rserver:
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image:
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repository: registry.hub.docker.com
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name: obiba/opal-rserver
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tag: latest
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pullPolicy: IfNotPresent
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resources:
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limits:
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cpu: 1
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memory: 2Gi
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containerPorts:
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- 6612
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- 6311
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mysql:
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persistence:
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enabled: false
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mysqlRootPassword: ParaD0xa
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mysqlUser: opal
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mysqlPassword: ?opal01!
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initializationFiles:
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opal-ids.sql: |-
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CREATE DATABASE IF NOT EXISTS opal_ids DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;
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GRANT ALL PRIVILEGES ON opal_ids.* TO "opal"@"%" IDENTIFIED BY "?opal01!";
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FLUSH PRIVILEGES;
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opal-data.sql: |-
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CREATE DATABASE IF NOT EXISTS opal_data DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;
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GRANT ALL PRIVILEGES ON opal_data.* TO "opal"@"%" IDENTIFIED BY "?opal01!";
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FLUSH PRIVILEGES;
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persistence:
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enabled: false
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retain: false
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nodeSelector: {
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deployPod: "true"
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}
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tolerations: []
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affinity: {}
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# Patterns to ignore when building packages.
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# This supports shell glob matching, relative path matching, and
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# negation (prefixed with !). Only one pattern per line.
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.DS_Store
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# Common VCS dirs
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.git/
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.gitignore
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.bzr/
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.bzrignore
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.hg/
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.hgignore
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.svn/
|
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# Common backup files
|
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*.swp
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*.bak
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*.tmp
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*~
|
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# Various IDEs
|
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.project
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.idea/
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*.tmproj
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apiVersion: v1
|
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appVersion: "1.0"
|
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description: RStudio stack
|
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name: rstudio
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version: 0.0.1
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sources:
|
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- https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm.git
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icon: https://raw.git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm/master/charts/rstudio/catalog-molgenis-rstudio.svg
|
||||
home: https://www.rocker.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
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@ -1,37 +0,0 @@
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# MOLGENIS - RStudio Helm Chart
|
||||
|
||||
An RStudio instance to support DataSHIELD users in setting up a central analysis server instance.
|
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|
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## Containers
|
||||
|
||||
This chart will deploy the following container:
|
||||
|
||||
- molgenis-rstudio (with DataSHIELD packages)
|
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|
||||
## Provisioning
|
||||
You can choose for the RStudio image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com.
|
||||
You need to fill out 2 properties to determine which repository you are going to use.
|
||||
|
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- ```rstudio.image.repository```
|
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- ```rstudio.image.tag```
|
||||
|
||||
You can do this in the questions in Rancher or in the ```values.yaml```.
|
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|
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## Development
|
||||
You can test in install the chart by executing:
|
||||
|
||||
```helm lint .```
|
||||
|
||||
To test if your helm chart-syntax is right and:
|
||||
|
||||
```helm install . --dry-run --debug```
|
||||
|
||||
To test if your hem chart works and:
|
||||
|
||||
```helm install .```
|
||||
|
||||
To deploy it on the cluster.
|
||||
|
||||
```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
|
||||
|
||||
To push it to the registry
|
|
@ -1,31 +0,0 @@
|
|||
|
||||
categories:
|
||||
- MOLGENIS
|
||||
questions:
|
||||
- variable: rstudio.environment
|
||||
label: Environment
|
||||
default: development
|
||||
type: enum
|
||||
options:
|
||||
- development
|
||||
- test
|
||||
- acceptence
|
||||
- production
|
||||
group: "Provisioning"
|
||||
- variable: rstudio.image.repository
|
||||
label: Registry
|
||||
default: "registry.hub.docker.com"
|
||||
description: "Select a registry to pull from"
|
||||
type: enum
|
||||
options:
|
||||
- "registry.hub.docker.com"
|
||||
- "registry.molgenis.org"
|
||||
required: true
|
||||
group: "Provisioning"
|
||||
- variable: rstudio.image.tag
|
||||
label: Version
|
||||
default: ""
|
||||
description: "Select a RStudio version (check the registry.molgenis.org or hub.docker.com for released tags)"
|
||||
type: string
|
||||
required: true
|
||||
group: "Provisioning"
|
|
@ -1,32 +0,0 @@
|
|||
{{/* vim: set filetype=mustache: */}}
|
||||
{{/*
|
||||
Expand the name of the chart.
|
||||
*/}}
|
||||
{{- define "rstudio.name" -}}
|
||||
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
Create a default fully qualified app name.
|
||||
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
||||
If release name contains chart name it will be used as a full name.
|
||||
*/}}
|
||||
{{- define "rstudio.fullname" -}}
|
||||
{{- if .Values.fullnameOverride -}}
|
||||
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
||||
{{- else -}}
|
||||
{{- $name := default .Chart.Name .Values.nameOverride -}}
|
||||
{{- if contains $name .Release.Name -}}
|
||||
{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||
{{- else -}}
|
||||
{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
Create chart name and version as used by the chart label.
|
||||
*/}}
|
||||
{{- define "rstudio.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
|
@ -1,46 +0,0 @@
|
|||
apiVersion: extensions/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
{{- with .Values.ingress.annotations }}
|
||||
annotations:
|
||||
{{ toYaml . | indent 4 }}
|
||||
{{- end }}
|
||||
name: {{ template "rstudio.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "rstudio.name" . }}
|
||||
chart: {{ template "rstudio.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ template "rstudio.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ template "rstudio.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
spec:
|
||||
containers:
|
||||
{{- with .Values.rstudio }}
|
||||
- name: {{ .name }}
|
||||
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: PASSWORD
|
||||
value: "{{ .adminPassword }}"
|
||||
ports:
|
||||
- containerPort: {{ .service.port }}
|
||||
livenessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .service.port }}
|
||||
initialDelaySeconds: 60
|
||||
periodSeconds: 5
|
||||
failureThreshold: 25
|
||||
successThreshold: 1
|
||||
{{- end }}
|
||||
|
||||
|
|
@ -1,36 +0,0 @@
|
|||
{{- if .Values.ingress.enabled }}
|
||||
{{- range .Values.ingress.hosts }}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
labels:
|
||||
app: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
|
||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
||||
release: "{{ $.Release.Name }}"
|
||||
heritage: "{{ $.Release.Service }}"
|
||||
annotations:
|
||||
{{- if .tls }}
|
||||
ingress.kubernetes.io/secure-backends: "true"
|
||||
{{- end }}
|
||||
{{- range $key, $value := .annotations }}
|
||||
{{ $key }}: {{ $value | quote }}
|
||||
{{- end }}
|
||||
spec:
|
||||
rules:
|
||||
- host: {{ .name }}
|
||||
http:
|
||||
paths:
|
||||
- path: {{ default "/" .path }}
|
||||
backend:
|
||||
serviceName: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
|
||||
servicePort: {{ $.Values.rstudio.service.port }}
|
||||
{{- if .tls }}
|
||||
tls:
|
||||
- hosts:
|
||||
- {{ .name }}
|
||||
secretName: {{ .tlsSecret }}
|
||||
{{- end }}
|
||||
---
|
||||
{{- end }}
|
||||
{{- end }}
|
|
@ -1,16 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
|
||||
labels:
|
||||
app: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
type: {{ .Values.rstudio.service.type }}
|
||||
ports:
|
||||
- name: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
|
||||
port: {{ .Values.rstudio.service.port }}
|
||||
selector:
|
||||
app: {{ template "rstudio.name" . }}
|
||||
release: {{ .Release.Name }}
|
|
@ -1,40 +0,0 @@
|
|||
# Default values for nexus.
|
||||
# This is a YAML-formatted file.
|
||||
# Declare variables to be passed into your templates.
|
||||
|
||||
replicaCount: 1
|
||||
|
||||
environment: production
|
||||
|
||||
rstudio:
|
||||
name: rstudio
|
||||
strategy:
|
||||
type: Recreate
|
||||
restartPolicy: Always
|
||||
adminPassword: ?01LifeCycle!
|
||||
image:
|
||||
repository: registry.hub.docker.com
|
||||
name: molgenis/rstudio
|
||||
tag: beta
|
||||
pullPolicy: Always
|
||||
service:
|
||||
name: rstudio
|
||||
type: ClusterIP
|
||||
port: 8787
|
||||
|
||||
ingress:
|
||||
enabled: true
|
||||
annotations: {
|
||||
kubernetes.io/ingress.class: "nginx",
|
||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||
}
|
||||
path: /
|
||||
hosts:
|
||||
- name: analysis.dev.molgenis.org
|
||||
tls: []
|
||||
|
||||
nodeSelector: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
Loading…
Reference in New Issue