added rstudio
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parent
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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 for MOLGENIS
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name: molgenis-rstudio
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version: 0.0.1
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sources:
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- https://github.com/molgenis/molgenis-ops-docker-helm.git
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icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-opencpu/catalog-molgenis-rstudio.svg
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home: https://www.rocker.org
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maintainers:
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- name: sidohaakma
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- name: fdlk
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# MOLGENIS - RStudio Helm Chart
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An RStudio instance to support DataSHIELD users in setting up a central analysis server instance.
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## Containers
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This chart will deploy the following container:
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- molgenis-rstudio (with DataSHIELD packages)
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## Provisioning
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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.
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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```
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You can do this in the questions in Rancher or in the ```values.yaml```.
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## Development
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You can test in install the chart by executing:
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```helm lint .```
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To test if your helm chart-syntax is right and:
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```helm install . --dry-run --debug```
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To test if your hem chart works and:
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```helm install .```
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To deploy it on the cluster.
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```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
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To push it to the registry
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categories:
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- MOLGENIS
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questions:
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- variable: rstudio.environment
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label: Environment
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default: development
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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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- acceptence
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- production
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group: "Provisioning"
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- variable: rstudio.image.repository
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label: Registry
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default: "registry.hub.docker.com"
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description: "Select a registry to pull from"
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type: enum
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options:
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- "registry.hub.docker.com"
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- "registry.molgenis.org"
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required: true
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group: "Provisioning"
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- variable: rstudio.image.tag
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label: Version
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default: ""
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description: "Select a RStudio 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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{{/* 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 "rstudio.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 "rstudio.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 "rstudio.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: extensions/v1beta1
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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 "rstudio.fullname" . }}
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labels:
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app: {{ template "rstudio.name" . }}
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chart: {{ template "rstudio.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 "rstudio.name" . }}
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release: {{ .Release.Name }}
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template:
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metadata:
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labels:
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app: {{ template "rstudio.name" . }}
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release: {{ .Release.Name }}
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spec:
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containers:
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{{- with .Values.rstudio }}
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- name: {{ .name }}
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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: {{ .service.port }}
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{{- end }}
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{{- if .Values.ingress.enabled }}
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{{- range .Values.ingress.hosts }}
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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.rstudio.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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annotations:
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{{- if .tls }}
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ingress.kubernetes.io/secure-backends: "true"
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{{- end }}
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{{- range $key, $value := .annotations }}
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{{ $key }}: {{ $value | quote }}
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{{- end }}
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spec:
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rules:
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{{- if .Values.environment -eq "development" }}
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- host: "analysis.dev.molgenis.org"
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{{- else if .Values.environment -eq "test" }}
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- host: "analysis.test.molgenis.org"
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{{- else if .Values.environment -eq "acceptance" }}
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- host: "analysis.accept.molgenis.org"
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{{- else }}
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- host: "analysis.molgenis.org"
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{{- end }}
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http:
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paths:
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- path: {{ default "/" .path }}
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backend:
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serviceName: {{ $.Values.rstudio.service.name }}
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servicePort: {{ $.Values.rstudio.service.port }}
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{{- if .tls }}
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tls:
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- hosts:
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- {{ .name }}
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secretName: {{ .tlsSecret }}
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{{- end }}
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---
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{{- end }}
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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: {{ .Values.rstudio.service.name }}
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labels:
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app: {{ .Values.rstudio.service.name }}
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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.rstudio.service.type }}
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loadBalancerSourceRanges:
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{{- range $index, $rule := .Values.rstudio.service.firewall }}
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- {{ $rule }}
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{{- end }}
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ports:
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- name: {{ .Values.rstudio.service.name }}
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port: {{ .Values.rstudio.service.port }}
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selector:
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app: {{ template "rstudio.name" . }}
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release: {{ .Release.Name }}
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# Default values for nexus.
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# This is a YAML-formatted file.
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# Declare variables to be passed into your templates.
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replicaCount: 1
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environment: production
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rstudio:
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environment: development
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name: rstudio
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strategy:
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type: Recreate
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restartPolicy: Always
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image:
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repository: registry.hub.docker.com
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name: molgenis/rstudio
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tag: stable
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pullPolicy: Always
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service:
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name: rstudio
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type: LoadBalancer
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port: 8787
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ingress:
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enabled: true
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annotations: {
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kubernetes.io/ingress.class: "nginx",
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nginx.ingress.kubernetes.io/proxy-body-size: "0"
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}
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path: /
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hosts:
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- name: analysis.molgenis.org
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tls: []
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nodeSelector: {}
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tolerations: []
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affinity: {}
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@ -2,7 +2,7 @@ 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: 0.5.4
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version: 0.0.1
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sources:
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- https://git.webhosting.rug.nl/opal/opal-ops-docker-helm.git
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icon: https://git.webhosting.rug.nl/opal/opal-ops-docker-helm/
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|
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@ -32,106 +32,4 @@ questions:
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type: string
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required: true
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group: "Provisioning"
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- variable: molgenis.adminPassword
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label: Administrator password
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default: ""
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description: "Enter an administrator password"
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type: password
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required: true
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group: "Provisioning"
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- variable: service.firewall.enabled
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label: Firewall enabled
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default: false
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description: "Firewall enabled (can be cluster or UMCG scoped)"
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type: boolean
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required: true
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group: "Services"
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show_subquestion_if: true
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subquestions:
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- variable: service.firewall.kind
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default: "umcg"
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description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
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type: enum
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required: true
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options:
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- umcg
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- cluster
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label: Firewall kind
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- variable: molgenis.advanced
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label: Advanced mode
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default: false
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description: "Do you want to override the default values in advanced mode"
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type: boolean
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required: true
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group: "Advanced"
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show_subquestion_if: true
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subquestions:
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- variable: molgenis.image.repository
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label: Registry
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default: "registry.hub.docker.com"
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description: "Select a registry to pull from"
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type: enum
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options:
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- "registry.hub.docker.com"
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- "registry.molgenis.org"
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required: true
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group: "Provisioning"
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- variable: molgenis.services.opencpu.host
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label: OpenCPU cluster
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default: "molgenis-opencpu.opencpu"
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description: "Specify the OpenCPU cluster"
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type: string
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required: true
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group: "Services"
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- variable: molgenis.services.postgres.embedded
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label: Postgres embedded
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default: true
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description: "Do you want an embedded postgres"
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type: boolean
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required: true
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group: "Services"
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- variable: molgenis.services.postgres.host
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label: Postgres cluster location
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default: "localhost"
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description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
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type: string
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required: true
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group: "Services"
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- variable: molgenis.services.postgres.scheme
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label: Database scheme
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default: "molgenis"
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description: "Set the database scheme"
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type: string
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required: true
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group: "Services"
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- variable: molgenis.services.postgres.user
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label: Database username
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default: "molgenis"
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description: "Set user of the database scheme"
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type: string
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required: true
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group: "Services"
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- variable: molgenis.services.postgres.password
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label: Database password
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default: "molgenis"
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description: "Set the password of the database scheme"
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type: string
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required: true
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group: "Services"
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- variable: persistence.retain
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default: false
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description: "Do you want to retain the persistent volume"
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type: boolean
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label: Retain volume
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group: "Persistence"
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- variable: persistence.molgenis.size
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default: "default"
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description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
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type: enum
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options:
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- "default"
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- "5Gi"
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- "10Gi"
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- "30Gi"
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label: Size MOLGENIS filestore
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group: "Persistence"
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|
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@ -42,13 +42,7 @@ spec:
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- name: admin.password
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value: "{{ .adminPassword }}"
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- name: CATALINA_OPTS
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{{- if eq .type.kind "small" }}
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value: "-Xmx{{ .type.small.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
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{{- else if eq .type.kind "medium"}}
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value: "-Xmx{{ .type.medium.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
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{{- else }}
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value: "-Xmx{{ .type.large.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
{{- end }}
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||||
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
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ports:
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- containerPort: 8080
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{{- if $.Values.persistence.enabled }}
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@ -73,13 +67,7 @@ spec:
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failureThreshold: 3
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successThreshold: 1
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resources:
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||||
{{- if eq .type.kind "small" }}
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||||
{{ toYaml .type.small.resources | indent 12 }}
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||||
{{- else if eq .type.kind "medium" }}
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||||
{{ toYaml .type.medium.resources | indent 12 }}
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||||
{{- else }}
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||||
{{ toYaml .type.large.resources | indent 12 }}
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||||
{{- end }}
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||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
{{- if .Values.persistence.enabled }}
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||||
|
|
|
|||
|
|
@ -26,19 +26,15 @@ spec:
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|||
{{- end }}
|
||||
{{- end }}
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rules:
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{{- if eq $.Values.opal.environment "development" }}
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- host: {{ .Release.Name }}.dev.opal.org
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||||
{{- else if eq $.Values.opal.environment "test" }}
|
||||
- host: {{ .Release.Name }}.test.opal.org
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||||
{{- else if eq $.Values.opal.environment "acceptance" }}
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||||
- host: {{ .Release.Name }}.accept.opal.org
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||||
{{- else }}
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||||
- host: {{ .Release.Name }}.opal.org
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||||
{{- end }}
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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:
|
||||
- path: {{ $ingressPath }}
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||||
backend:
|
||||
serviceName: {{ $fullName }}
|
||||
servicePort: {{ $.Values.service.port }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
|
|||
|
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@ -15,11 +15,5 @@ spec:
|
|||
- ReadWriteMany
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||||
resources:
|
||||
requests:
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||||
{{- if eq .Values.opal.type.kind "small" }}
|
||||
storage: {{ .Values.mysql.type.small.persistence.size }}
|
||||
{{- else if eq .Values.opal.type.kind "medium" }}
|
||||
storage: {{ .Values.mysql.type.medium.persistence.size }}
|
||||
{{- else }}
|
||||
storage: {{ .Values.mysql.type.large.persistence.size }}
|
||||
{{- end }}
|
||||
storage: {{ .Values.mysql.persistence.size }}
|
||||
{{- end }}
|
||||
|
|
@ -15,11 +15,5 @@ spec:
|
|||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
{{- if eq .Values.opal.type.kind "small" }}
|
||||
storage: {{ .Values.opal.type.small.persistence.size }}
|
||||
{{- else if eq .Values.opal.type.kind "medium" }}
|
||||
storage: {{ .Values.opal.type.medium.persistence.size }}
|
||||
{{- else }}
|
||||
storage: {{ .Values.opal.type.large.persistence.size }}
|
||||
{{- end }}
|
||||
storage: {{ .Values.opal.persistence.size }}
|
||||
{{- end }}
|
||||
|
|
@ -4,68 +4,30 @@ replicaCount: 1
|
|||
|
||||
service:
|
||||
type: LoadBalancer
|
||||
firewall:
|
||||
enabled: false
|
||||
kind: "umcg"
|
||||
umcg:
|
||||
rules:
|
||||
- 127.0.0.1/32
|
||||
cluster:
|
||||
rules:
|
||||
- 127.0.0.1/32
|
||||
port: 8080
|
||||
|
||||
ingress:
|
||||
enabled: true
|
||||
annotations:
|
||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||
# This will be used again when external domains need be attached to the instance
|
||||
# hosts:
|
||||
# - name: test
|
||||
hosts:
|
||||
- name: opal.dev.molgenis.org
|
||||
path: /
|
||||
tls: []
|
||||
|
||||
opal:
|
||||
advanced: false
|
||||
type:
|
||||
kind: medium
|
||||
small:
|
||||
javaOpts:
|
||||
maxHeapSpace: "2g"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 2
|
||||
memory: 2Gi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 2Gi
|
||||
persistence:
|
||||
size: 5Gi
|
||||
medium:
|
||||
javaOpts:
|
||||
maxHeapSpace: "3g"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 3
|
||||
memory: 3Gi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 3Gi
|
||||
persistence:
|
||||
size: 10Gi
|
||||
large:
|
||||
javaOpts:
|
||||
maxHeapSpace: "4g"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 4
|
||||
memory: 4Gi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 4Gi
|
||||
persistence:
|
||||
size: 30Gi
|
||||
environment: test
|
||||
javaOpts:
|
||||
maxHeapSpace: "4g"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 4
|
||||
memory: 4Gi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 4Gi
|
||||
persistence:
|
||||
size: 10Gi
|
||||
image:
|
||||
repository: registry.hub.docker.com
|
||||
name: obiba/opal
|
||||
|
|
@ -86,6 +48,10 @@ rserver:
|
|||
tag: latest
|
||||
pullPolicy: IfNotPresent
|
||||
|
||||
mysql:
|
||||
persistence:
|
||||
size: 10Gi
|
||||
|
||||
persistence:
|
||||
enabled: true
|
||||
retain: false
|
||||
|
|
|
|||
Loading…
Reference in New Issue