refactor: Move charts to charts directory
This commit is contained in:
Fleur Kelpin
parent
2a1e9eacbb
commit
2e4e397aff
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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: HTTPD for MOLGENIS
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name: molgenis-httpd
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version: 0.1.0
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sources:
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- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
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icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg
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# MOLGENIS - HTTPD Helm Chart
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HTTPD (web)server for kubernetes to deploy on a kubernetes cluster with NFS-share
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## Chart Details
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This chart will deploy:
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- 1 HTTPD container
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## Installing the Chart
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etc.
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categories:
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- MOLGENIS
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questions:
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- variable: ingress.hosts[0].name
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default: "test.molgenis.org"
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description: "Hostname for your stack"
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type: hostname
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required: true
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group: "Services and Load Balancing"
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label: Hostname
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- variable: httpd.hostname
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default: "test.molgenis.org"
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description: "Hostname for your services (comma separated, example: [hostname]:[port])"
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type: string
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required: false
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group: "Apache configuration"
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label: Hostname
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- variable: httpd.proxy
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default: ""
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description: "Proxy for your services (comma separated, example: [service]:[port]:[path])"
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type: string
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required: false
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group: "Apache configuration"
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label: Proxy
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- variable: httpd.redirect
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default: ""
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description: "Redirection urls for your services (comma separated, example: [redirection_url])"
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type: string
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required: false
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group: "Apache configuration"
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label: Redirection
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@ -1,19 +0,0 @@
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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 "httpd.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:$NODE_PORT
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{{- else if contains "LoadBalancer" .Values.service.type }}
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NOTE: It may take a few minutes for the LoadBalancer IP to be available.
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You can watch the status of by running 'kubectl get svc -w {{ template "httpd.fullname" . }}'
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export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "httpd.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 "httpd.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 "httpd.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 "httpd.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 "httpd.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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name: {{ template "httpd.fullname" . }}
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labels:
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app: {{ template "httpd.name" . }}
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chart: {{ template "httpd.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 "httpd.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 "httpd.name" . }}
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release: {{ .Release.Name }}
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spec:
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containers:
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- name: {{ .Chart.Name }}
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image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
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imagePullPolicy: {{ .Values.image.pullPolicy }}
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ports:
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- name: {{ .Values.service.name }}
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containerPort: {{ .Values.service.port }}
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env:
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- name: SERVER_NAME
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value: "{{ .Values.httpd.hostname }}"
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- name: PROXY_SERVICE
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value: "{{ .Values.httpd.proxy }}"
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- name: REDIRECT_URL
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value: "{{ .Values.httpd.redirect }}"
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livenessProbe:
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httpGet:
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path: /
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port: http
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readinessProbe:
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httpGet:
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path: /
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port: http
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resources:
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{{ toYaml .Values.resources | indent 12 }}
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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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{{- 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: {{ template "httpd.fullname" $ }}
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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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- host: {{ .name }}
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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: {{ template "httpd.fullname" $ }}
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servicePort: 80
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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: {{ template "httpd.fullname" . }}
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labels:
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app: {{ template "httpd.name" . }}
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chart: {{ template "httpd.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: {{ .Values.service.name }}
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port: {{ .Values.service.port }}
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selector:
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app: {{ template "httpd.name" . }}
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release: {{ .Release.Name }}
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# Default values for jenkins.
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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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image:
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repository: registry.webhosting.rug.nl/molgenis/httpd
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tag: lts
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pullPolicy: Always
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service:
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name: httpd
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type: ClusterIP
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port: 80
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httpd:
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proxy: httpd:80:/
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redirect: redirect.molgenis.local
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hostname: test.molgenis.local
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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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# kubernetes.io/tls-acme: "true"
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path: /
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hosts:
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- name: test.molgenis.org
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tls: []
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# - secretName: chart-example-tls
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# hosts:
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# - chart-example.local
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resources: {}
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# We usually recommend not to specify default resources and to leave this as a conscious
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# choice for the user. This also increases chances charts run on environments with little
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# resources, such as Minikube. If you do want to specify resources, uncomment the following
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# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
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# limits:
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# cpu: 100m
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# memory: 128Mi
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# requests:
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# cpu: 100m
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# memory: 128Mi
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nodeSelector: {}
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tolerations: []
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affinity: {}
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name: molgenis-jenkins
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home: https://jenkins.io/
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version: 0.7.1
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appVersion: 2.121
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description: Molgenis installation for the jenkins chart.
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sources:
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- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
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icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg
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# Molgenis Jenkins Helm Chart
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Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin.
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Wraps [the kuberenetes jenkins chart](https://github.com/kubernetes/charts/tree/master/stable/jenkins), see documentation there!
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## Chart Details
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This chart will do the following:
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* 1 x Jenkins Master with port 8080 exposed on an external ClusterIP
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* All using Kubernetes Deployments
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## Installing the Chart
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Usually, you'll be deploying this to the molgenis cluster.
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In the [Rancher Catalog](https://rancher.molgenis.org:7443/g/catalog), add the latest version of this repository.
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In the [molgenis cluster management page](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/apps), choose the
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catalog, pick the molgenis-jenkins app from the catalog and deploy it.
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## Configuration
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When deploying, you can paste values into the Rancher Answers to override the defaults in this chart.
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Array values can be added as {value, value, value}.
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```
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jenkins.Master.HostName=jenkins.molgenis.org
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jenkins.Master.AdminPassword=pa$$word
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jenkins.Persistence.Enabled=false
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jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29}
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jenkins.Master.Security.UseGitHub=false
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## if UseGitHub=true
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jenkins.Master.Security.GitHub.ClientID=id
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jenkins.Master.Security.GitHub.ClientSecret=S3cr3t
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## end UseGitHub=true
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PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
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```
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You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
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> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
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### GitHub Authentication delegation
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You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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### Secrets
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
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You can override the values at deploy time but otherwise also configure them
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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#### Vault
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The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
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| Parameter | Description | Default |
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| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
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| `secret.vault.token` | Token to log into the hashicorp vault | `xxxx` |
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| `secret.vault.addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
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| `secret.vault.skipVerify` | Skip verification of the https connection | `1` |
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#### GitHub
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Token used by Jenkins to authenticate on GitHub.
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| Parameter | Description | Default |
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| --------------------- | ------------------------ | ------------------ |
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| `secret.gitHub.user` | username for the account | `molgenis-jenkins` |
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| `secret.gitHub.token` | token for the account | `xxxx` |
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#### Gogs
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Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
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| Parameter | Description | Default |
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| ------------------- | ------------------------ | --------- |
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| `secret.gogs.user` | username for the account | `p281392` |
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| `secret.gogs.token` | token for the account | `xxxx` |
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#### Legacy:
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##### Docker Hub
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Account used in pipeline builds to push docker images to `hub.docker.com`.
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> They should read `secret/gcc/account/dockerhub` from vault instead!
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| Parameter | Description | Default |
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| --------------------------- | ------------------------ | --------------- |
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| `secret.dockerHub.user` | username for the account | `molgenisci` |
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| `secret.dockerHub.password` | password for the account | `xxxx` |
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##### Registry
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Account used in pipeline builds to push docker images to `registry.molgenis.org`.
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> They should read `secret/ops/account/nexus` from vault instead!
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| Parameter | Description | Default |
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| --------------------------- | ------------------------ | --------- |
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| `secret.dockerHub.user` | username for the account | `admin` |
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| `secret.dockerHub.password` | password for the account | `xxxx` |
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## Command line use
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Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
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Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart.
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For example,
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```bash
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$ helm install --name jenkins -f values.yaml molgenis-jenkins
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```
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> **Tip**: You can use the default [values.yaml](values.yaml)
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dependencies:
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- name: jenkins
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repository: https://kubernetes-charts.storage.googleapis.com/
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version: 0.18.0
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digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
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generated: 2018-09-27T11:00:15.795416984+02:00
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dependencies:
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- name: jenkins
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version: ^0.16
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repository: https://kubernetes-charts.storage.googleapis.com/
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To be able to run helm inside a jenkins pod, you'll need to
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* create a role in the namespace where tiller is installed
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* bind that role to the user that jenkins pods run as
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This directory contains yaml for these resources.
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See also https://github.com/helm/helm/blob/master/docs/rbac.md
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apiVersion: rbac.authorization.k8s.io/v1beta1
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kind: RoleBinding
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metadata:
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name: tiller-jenkins-binding
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namespace: kube-system
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roleRef:
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apiGroup: rbac.authorization.k8s.io
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kind: Role
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name: tiller-user
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subjects:
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- kind: ServiceAccount
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name: default
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namespace: molgenis-jenkins
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
apiVersion: rbac.authorization.k8s.io/v1beta1
|
||||
kind: Role
|
||||
metadata:
|
||||
name: tiller-user
|
||||
namespace: kube-system
|
||||
rules:
|
||||
- apiGroups:
|
||||
- ""
|
||||
resources:
|
||||
- pods/portforward
|
||||
verbs:
|
||||
- create
|
||||
- apiGroups:
|
||||
- ""
|
||||
resources:
|
||||
- pods
|
||||
verbs:
|
||||
- list
|
||||
|
|
@ -1,283 +0,0 @@
|
|||
{{- define "override_config_map" }}
|
||||
apiVersion: v1
|
||||
kind: ConfigMap
|
||||
metadata:
|
||||
name: {{ template "jenkins.fullname" . }}
|
||||
data:
|
||||
config.xml: |-
|
||||
<?xml version='1.0' encoding='UTF-8'?>
|
||||
<hudson>
|
||||
<disabledAdministrativeMonitors/>
|
||||
<version>{{ .Values.Master.ImageTag }}</version>
|
||||
<numExecutors>0</numExecutors>
|
||||
<mode>NORMAL</mode>
|
||||
<useSecurity>{{ .Values.Master.UseSecurity }}</useSecurity>
|
||||
<authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
|
||||
<denyAnonymousReadAccess>true</denyAnonymousReadAccess>
|
||||
</authorizationStrategy>
|
||||
{{- if .Values.Master.Security.UseGitHub }}
|
||||
<securityRealm class="org.jenkinsci.plugins.GithubSecurityRealm">
|
||||
<githubWebUri>https://github.com</githubWebUri>
|
||||
<githubApiUri>https://api.github.com</githubApiUri>
|
||||
<clientID>{{ .Values.Master.Security.GitHub.ClientID }}</clientID>
|
||||
<clientSecret>{{ .Values.Master.Security.GitHub.ClientSecret }}</clientSecret>
|
||||
<oauthScopes>read:org,user:email</oauthScopes>
|
||||
</securityRealm>
|
||||
{{- else }}
|
||||
<securityRealm class="hudson.security.LegacySecurityRealm"/>
|
||||
{{- end }}
|
||||
<disableRememberMe>false</disableRememberMe>
|
||||
<projectNamingStrategy class="jenkins.model.ProjectNamingStrategy$DefaultProjectNamingStrategy"/>
|
||||
<workspaceDir>${JENKINS_HOME}/workspace/${ITEM_FULLNAME}</workspaceDir>
|
||||
<buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
|
||||
<markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
|
||||
<jdks/>
|
||||
<primaryView>dev</primaryView>
|
||||
<viewsTabBar class="hudson.views.DefaultViewsTabBar"/>
|
||||
<myViewsTabBar class="hudson.views.DefaultMyViewsTabBar"/>
|
||||
<clouds>
|
||||
<org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud plugin="kubernetes@{{ template "jenkins.kubernetes-version" . }}">
|
||||
<name>kubernetes</name>
|
||||
<templates>
|
||||
{{- range $podName, $pod := .Values.Pods }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
|
||||
<inheritFrom>{{ $pod.InheritFrom | default "" }}</inheritFrom>
|
||||
<name>{{ $podName }}</name>
|
||||
<instanceCap>2147483647</instanceCap>
|
||||
<idleMinutes>0</idleMinutes>
|
||||
<label>{{ .Label }}</label>
|
||||
<nodeSelector>
|
||||
{{- $local := dict "first" true }}
|
||||
{{- range $key, $value := .NodeSelector }}
|
||||
{{- if not $local.first }},{{- end }}
|
||||
{{- $key }}={{ $value }}
|
||||
{{- $_ := set $local "first" false }}
|
||||
{{- end }}</nodeSelector>
|
||||
<nodeUsageMode>{{ .NodeUsageMode }}</nodeUsageMode>
|
||||
<volumes>
|
||||
{{- range $index, $volume := .volumes }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.volumes.{{ .type }}Volume>
|
||||
{{- range $key, $value := $volume }}{{- if not (eq $key "type") }}
|
||||
<{{ $key }}>{{ $value }}</{{ $key }}>
|
||||
{{- end }}{{- end }}
|
||||
</org.csanchez.jenkins.plugins.kubernetes.volumes.{{ .type }}Volume>
|
||||
{{- end }}
|
||||
</volumes>
|
||||
<containers>
|
||||
{{- range $containerName, $container := .Containers }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
|
||||
<name>{{ $containerName }}</name>
|
||||
<image>{{ .Image }}:{{ .ImageTag | default "latest" }}</image>
|
||||
<ports>
|
||||
{{- range $index, $envVar := .Ports }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.PortMapping>
|
||||
<name>{{ .name }}</name>
|
||||
<containerPort>{{ .containerPort }}</containerPort>
|
||||
<hostPort>{{ .hostPort }}</hostPort>
|
||||
</org.csanchez.jenkins.plugins.kubernetes.PortMapping>
|
||||
{{- end }}
|
||||
</ports>
|
||||
{{- if .Privileged }}
|
||||
<privileged>true</privileged>
|
||||
{{- else }}
|
||||
<privileged>false</privileged>
|
||||
{{- end }}
|
||||
{{- if .AlwaysPullImage }}
|
||||
<alwaysPullImage>true</alwaysPullImage>
|
||||
{{- else }}
|
||||
<alwaysPullImage>false</alwaysPullImage>
|
||||
{{- end }}
|
||||
<workingDir>{{ .WorkingDir | default "" }}</workingDir>
|
||||
<command>{{ .Command | default "" }}</command>
|
||||
<args>{{ .Args | default "" }}</args>
|
||||
{{- if .TTY }}
|
||||
<ttyEnabled>true</ttyEnabled>
|
||||
{{- else }}
|
||||
<ttyEnabled>false</ttyEnabled>
|
||||
{{- end }}
|
||||
<envVars>
|
||||
{{- range $index, $envVar := .EnvVars }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
|
||||
{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }}
|
||||
<{{ $key }}>{{ $value }}</{{ $key }}>
|
||||
{{- end }}{{- end }}
|
||||
</org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
|
||||
{{- end }}
|
||||
</envVars>
|
||||
{{- if .resources }}
|
||||
{{- if .resources.requests }}
|
||||
<resourceRequestCpu>{{ .resources.requests.cpu | default "" }}</resourceRequestCpu>
|
||||
<resourceRequestMemory>{{ .resources.requests.memory | default "" }}</resourceRequestMemory>
|
||||
{{- end }}
|
||||
{{- if .resources.limits }}
|
||||
<resourceLimitCpu>{{ .resources.limits.cpu | default "" }}</resourceLimitCpu>
|
||||
<resourceLimitMemory>{{ .resources.limits.memory | default "" }}</resourceLimitMemory>
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
</org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
|
||||
{{- end }}
|
||||
</containers>
|
||||
<envVars>
|
||||
<org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
|
||||
<key>JENKINS_URL</key>
|
||||
<value>http://{{ template "jenkins.fullname" $ }}:{{$.Values.Master.ServicePort}}{{ default "" $.Values.Master.JenkinsUriPrefix }}</value>
|
||||
</org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
|
||||
{{- range $index, $envVar := .EnvVars }}
|
||||
<org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
|
||||
{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }}
|
||||
<{{ $key }}>{{ $value }}</{{ $key }}>
|
||||
{{- end }}{{- end }}
|
||||
</org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
|
||||
{{- end }}
|
||||
</envVars>
|
||||
<annotations/>
|
||||
{{- if .ImagePullSecret }}
|
||||
<imagePullSecrets>
|
||||
<org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
|
||||
<name>{{ .ImagePullSecret }}</name>
|
||||
</org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
|
||||
</imagePullSecrets>
|
||||
{{- else }}
|
||||
<imagePullSecrets/>
|
||||
{{- end }}
|
||||
<nodeProperties/>
|
||||
</org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
|
||||
{{- end }}
|
||||
</templates>
|
||||
<serverUrl>https://kubernetes.default</serverUrl>
|
||||
<skipTlsVerify>false</skipTlsVerify>
|
||||
<namespace>{{ .Release.Namespace }}</namespace>
|
||||
<jenkinsUrl>http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }}</jenkinsUrl>
|
||||
<jenkinsTunnel>{{ template "jenkins.fullname" . }}-agent:50000</jenkinsTunnel>
|
||||
<containerCap>50</containerCap>
|
||||
<retentionTimeout>5</retentionTimeout>
|
||||
<connectTimeout>0</connectTimeout>
|
||||
<readTimeout>0</readTimeout>
|
||||
</org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud>
|
||||
</clouds>
|
||||
<quietPeriod>5</quietPeriod>
|
||||
<scmCheckoutRetryCount>0</scmCheckoutRetryCount>
|
||||
<views>
|
||||
<hudson.model.AllView>
|
||||
<owner class="hudson" reference="../../.."/>
|
||||
<name>all</name>
|
||||
<filterExecutors>false</filterExecutors>
|
||||
<filterQueue>false</filterQueue>
|
||||
<properties class="hudson.model.View$PropertyList"/>
|
||||
</hudson.model.AllView>
|
||||
{{- range $viewName, $view := .Values.Master.Views }}
|
||||
<listView>
|
||||
<owner class="hudson" reference="../../.."/>
|
||||
<name>{{ $viewName }}</name>
|
||||
<filterExecutors>false</filterExecutors>
|
||||
<filterQueue>false</filterQueue>
|
||||
<properties class="hudson.model.View$PropertyList"/>
|
||||
<jobNames>
|
||||
<comparator class="hudson.util.CaseInsensitiveComparator" reference="../../../listView/jobNames/comparator"/>
|
||||
{{- range $index, $job := $view }}
|
||||
<string>{{ $job }}</string>
|
||||
{{- end }}
|
||||
</jobNames>
|
||||
<jobFilters/>
|
||||
<columns>
|
||||
<hudson.views.StatusColumn/>
|
||||
<hudson.views.WeatherColumn/>
|
||||
<hudson.views.JobColumn/>
|
||||
<hudson.views.LastSuccessColumn/>
|
||||
<hudson.views.LastFailureColumn/>
|
||||
<hudson.views.LastDurationColumn/>
|
||||
<hudson.views.BuildButtonColumn/>
|
||||
<hudson.plugins.favorite.column.FavoriteColumn plugin="favorite@2.3.2"/>
|
||||
</columns>
|
||||
<recurse>false</recurse>
|
||||
</listView>
|
||||
{{- end }}
|
||||
</views>
|
||||
<primaryView>{{ .Values.Master.DefaultView }}</primaryView>
|
||||
<slaveAgentPort>50000</slaveAgentPort>
|
||||
<disabledAgentProtocols>
|
||||
{{- range .Values.Master.DisabledAgentProtocols }}
|
||||
<string>{{ . }}</string>
|
||||
{{- end }}
|
||||
</disabledAgentProtocols>
|
||||
<label></label>
|
||||
{{- if .Values.Master.CSRF.DefaultCrumbIssuer.Enabled }}
|
||||
<crumbIssuer class="hudson.security.csrf.DefaultCrumbIssuer">
|
||||
{{- if .Values.Master.CSRF.DefaultCrumbIssuer.ProxyCompatability }}
|
||||
<excludeClientIPFromCrumb>true</excludeClientIPFromCrumb>
|
||||
{{- end }}
|
||||
</crumbIssuer>
|
||||
{{- end }}
|
||||
<nodeProperties/>
|
||||
<globalNodeProperties/>
|
||||
<noUsageStatistics>true</noUsageStatistics>
|
||||
</hudson>
|
||||
{{- if .Values.Master.ScriptApproval }}
|
||||
scriptapproval.xml: |-
|
||||
<?xml version='1.0' encoding='UTF-8'?>
|
||||
<scriptApproval plugin="script-security@1.27">
|
||||
<approvedScriptHashes/>
|
||||
<approvedSignatures>
|
||||
{{- range $key, $val := .Values.Master.ScriptApproval }}
|
||||
<string>{{ $val }}</string>
|
||||
{{- end }}
|
||||
</approvedSignatures>
|
||||
<aclApprovedSignatures/>
|
||||
<approvedClasspathEntries/>
|
||||
<pendingScripts/>
|
||||
<pendingSignatures/>
|
||||
<pendingClasspathEntries/>
|
||||
</scriptApproval>
|
||||
{{- end }}
|
||||
jenkins.CLI.xml: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<jenkins.CLI>
|
||||
{{- if .Values.Master.CLI }}
|
||||
<enabled>true</enabled>
|
||||
{{- else }}
|
||||
<enabled>false</enabled>
|
||||
{{- end }}
|
||||
</jenkins.CLI>
|
||||
apply_config.sh: |-
|
||||
mkdir -p /usr/share/jenkins/ref/secrets/;
|
||||
echo "false" > /usr/share/jenkins/ref/secrets/slave-to-master-security-kill-switch;
|
||||
cp -n /var/jenkins_config/config.xml /var/jenkins_home;
|
||||
cp -n /var/jenkins_config/jenkins.CLI.xml /var/jenkins_home;
|
||||
{{- if .Values.Master.InstallPlugins }}
|
||||
# Install missing plugins
|
||||
cp /var/jenkins_config/plugins.txt /var/jenkins_home;
|
||||
rm -rf /usr/share/jenkins/ref/plugins/*.lock
|
||||
/usr/local/bin/install-plugins.sh `echo $(cat /var/jenkins_home/plugins.txt)`;
|
||||
# Copy plugins to shared volume
|
||||
cp -n /usr/share/jenkins/ref/plugins/* /var/jenkins_plugins;
|
||||
{{- end }}
|
||||
{{- if .Values.Master.ScriptApproval }}
|
||||
cp -n /var/jenkins_config/scriptapproval.xml /var/jenkins_home/scriptApproval.xml;
|
||||
{{- end }}
|
||||
{{- if .Values.Master.InitScripts }}
|
||||
mkdir -p /var/jenkins_home/init.groovy.d/;
|
||||
cp -n /var/jenkins_config/*.groovy /var/jenkins_home/init.groovy.d/
|
||||
{{- end }}
|
||||
{{- if .Values.Master.CredentialsXmlSecret }}
|
||||
cp -n /var/jenkins_credentials/credentials.xml /var/jenkins_home;
|
||||
{{- end }}
|
||||
{{- if .Values.Master.SecretsFilesSecret }}
|
||||
cp -n /var/jenkins_secrets/* /usr/share/jenkins/ref/secrets;
|
||||
{{- end }}
|
||||
{{- if .Values.Master.Jobs }}
|
||||
for job in $(ls /var/jenkins_jobs); do
|
||||
mkdir -p /var/jenkins_home/jobs/$job
|
||||
cp -n /var/jenkins_jobs/$job /var/jenkins_home/jobs/$job/config.xml
|
||||
done
|
||||
{{- end }}
|
||||
{{- range $key, $val := .Values.Master.InitScripts }}
|
||||
init{{ $key }}.groovy: |-
|
||||
{{ $val | indent 4 }}
|
||||
{{- end }}
|
||||
plugins.txt: |-
|
||||
{{- if .Values.Master.InstallPlugins }}
|
||||
{{- range $index, $val := .Values.Master.InstallPlugins }}
|
||||
{{ $val | indent 4 }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
# this is the jenkins id.
|
||||
name: "molgenis-jenkins-dockerhub-secret"
|
||||
labels:
|
||||
# so we know what type it is.
|
||||
"jenkins.io/credentials-type": "usernamePassword"
|
||||
annotations: {
|
||||
# description - can not be a label as spaces are not allowed
|
||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
|
||||
}
|
||||
type: Opaque
|
||||
data:
|
||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
# this is the jenkins id.
|
||||
name: "molgenis-jenkins-github-secret"
|
||||
labels:
|
||||
# so we know what type it is.
|
||||
"jenkins.io/credentials-type": "usernamePassword"
|
||||
annotations: {
|
||||
# description - can not be a label as spaces are not allowed
|
||||
"jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
|
||||
}
|
||||
type: Opaque
|
||||
data:
|
||||
username: {{ .Values.secret.gitHub.user | b64enc | quote }}
|
||||
password: {{ .Values.secret.gitHub.token | b64enc | quote }}
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
# this is the jenkins id.
|
||||
name: "molgenis-jenkins-gogs-secret"
|
||||
labels:
|
||||
# so we know what type it is.
|
||||
"jenkins.io/credentials-type": "usernamePassword"
|
||||
annotations: {
|
||||
# description - can not be a label as spaces are not allowed
|
||||
"jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
|
||||
}
|
||||
type: Opaque
|
||||
data:
|
||||
username: {{ .Values.secret.gogs.user | b64enc | quote }}
|
||||
password: {{ .Values.secret.gogs.token | b64enc | quote }}
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
name: molgenis-jenkins-registry-secret
|
||||
labels:
|
||||
app: {{ template "jenkins.fullname" . }}
|
||||
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||
release: "{{ .Release.Name }}"
|
||||
heritage: "{{ .Release.Service }}"
|
||||
annotations: {
|
||||
# description - can not be a label as spaces are not allowed
|
||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
|
||||
}
|
||||
type: Opaque
|
||||
data:
|
||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
||||
|
|
@ -1,14 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
name: molgenis-pipeline-vault-secret
|
||||
labels:
|
||||
app: {{ template "jenkins.fullname" . }}
|
||||
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||
release: "{{ .Release.Name }}"
|
||||
heritage: "{{ .Release.Service }}"
|
||||
type: Opaque
|
||||
data:
|
||||
token: {{ .Values.secret.vault.token | b64enc | quote }}
|
||||
addr: {{ .Values.secret.vault.addr | b64enc | quote }}
|
||||
skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
|
||||
|
|
@ -1,608 +0,0 @@
|
|||
jenkins:
|
||||
Master:
|
||||
HostName: jenkins.molgenis.org
|
||||
ServiceType: ClusterIP
|
||||
InstallPlugins:
|
||||
- kubernetes:1.12.6
|
||||
- workflow-aggregator:2.5
|
||||
- workflow-job:2.25
|
||||
- credentials-binding:1.16
|
||||
- git:3.9.1
|
||||
- github-branch-source:2.3.6
|
||||
- kubernetes-credentials-provider:0.10
|
||||
- blueocean:1.8.3
|
||||
- github-oauth:0.29
|
||||
- gogs-webhook:1.0.14
|
||||
- github-scm-trait-commit-skip:0.1.1
|
||||
Security:
|
||||
UseGitHub: false
|
||||
GitHub:
|
||||
ClientID: ""
|
||||
ClienSecret: ""
|
||||
DefaultView: dev
|
||||
Views:
|
||||
dev:
|
||||
- molgenis
|
||||
ops:
|
||||
- molgenis-ops-docker-httpd
|
||||
- molgenis-ops-docker-maven
|
||||
- molgenis-ops-docker-node
|
||||
- molgenis-ops-tools
|
||||
- molgenis-ops-tomcat
|
||||
Jobs: |-
|
||||
molgenis: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<jenkins.branch.OrganizationFolder plugin="branch-api@2.0.20">
|
||||
<actions/>
|
||||
<description></description>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
<jenkins.branch.NoTriggerOrganizationFolderProperty>
|
||||
<branches>.*</branches>
|
||||
</jenkins.branch.NoTriggerOrganizationFolderProperty>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.OrganizationFolderViewHolder">
|
||||
<owner reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon">
|
||||
<owner class="jenkins.branch.OrganizationFolder" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers>
|
||||
<com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger plugin="cloudbees-folder@6.5.1">
|
||||
<spec>H H * * *</spec>
|
||||
<interval>86400000</interval>
|
||||
</com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger>
|
||||
</triggers>
|
||||
<disabled>false</disabled>
|
||||
<navigators>
|
||||
<org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator plugin="github-branch-source@2.3.6">
|
||||
<repoOwner>molgenis</repoOwner>
|
||||
<credentialsId>molgenis-jenkins-github-secret</credentialsId>
|
||||
<traits>
|
||||
<org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
</org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
</org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
||||
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
||||
</navigators>
|
||||
<projectFactories>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory plugin="workflow-multibranch@2.19">
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory>
|
||||
</projectFactories>
|
||||
<buildStrategies/>
|
||||
</jenkins.branch.OrganizationFolder>
|
||||
molgenis-ops-docker-httpd: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>HTTPD server that can be used for redirection and proxieing</description>
|
||||
<displayName>molgenis-ops-docker-httpd</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>a756941d-6c9d-4492-bcf9-327041764be6</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-httpd.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-docker-node: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>NodeJS build container with Curl</description>
|
||||
<displayName>molgenis-ops-docker-node</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>a756941d-6c9d-4492-bcf9-327041764be6</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-node.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-docker-maven: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MAVEN build container with RPMbuild and Curl</description>
|
||||
<displayName>molgenis-ops-docker-maven</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-maven.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-tomcat: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MOLGENIS tomcat package to manage tomcat version on CentOS</description>
|
||||
<displayName>molgenis-ops-tomcat</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tomcat.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-tools: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MOLGENIS operations tools-package to configure firewall, apache, sudoers, etc.</description>
|
||||
<displayName>molgenis-ops-tools</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tools.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
# Kubernetes secret that contains a 'credentials.xml' for Jenkins
|
||||
# CredentialsXmlSecret: jenkins-credentials
|
||||
# Kubernetes secret that contains files to be put in the Jenkins 'secrets' directory,
|
||||
# useful to manage encryption keys used for credentials.xml for instance (such as
|
||||
# master.key and hudson.util.Secret)
|
||||
# SecretsFilesSecret: jenkins-secrets
|
||||
CustomConfigMap: true
|
||||
rbac:
|
||||
install: true
|
||||
Pods:
|
||||
molgenis:
|
||||
Label: molgenis
|
||||
NodeUsageMode: NORMAL
|
||||
volumes:
|
||||
- type: HostPath
|
||||
hostPath: "/var/run/docker.sock"
|
||||
mountPath: "/var/run/docker.sock"
|
||||
Containers:
|
||||
maven:
|
||||
Image: "registry.webhosting.rug.nl/molgenis/maven"
|
||||
ImageTag: lts
|
||||
AlwaysPullImage: true
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
resources:
|
||||
requests:
|
||||
cpu: "1"
|
||||
memory: "4Gi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: MAVEN_OPTS
|
||||
value: "-Duser.home=/home/jenkins"
|
||||
- type: KeyValue
|
||||
key: MAVEN_CONFIG
|
||||
value: "/home/jenkins/.m2"
|
||||
alpine:
|
||||
Image: "spotify/alpine"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
vault:
|
||||
Image: "vault"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
EnvVars:
|
||||
- type: Secret
|
||||
key: VAULT_TOKEN
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: token
|
||||
- type: Secret
|
||||
key: VAULT_SKIP_VERIFY
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: skipVerify
|
||||
- type: Secret
|
||||
key: VAULT_ADDR
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: addr
|
||||
helm:
|
||||
Image: "lachlanevenson/k8s-helm"
|
||||
ImageTag: "v2.10.0"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
NodeSelector: {}
|
||||
node:
|
||||
Label: node-carbon
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
Containers:
|
||||
node:
|
||||
Image: "registry.webhosting.rug.nl/molgenis/node"
|
||||
ImageTag: lts
|
||||
AlwaysPullImage: true
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
vault:
|
||||
Image: "vault"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
EnvVars:
|
||||
- type: Secret
|
||||
key: VAULT_TOKEN
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: token
|
||||
- type: Secret
|
||||
key: VAULT_SKIP_VERIFY
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: skipVerify
|
||||
- type: Secret
|
||||
key: VAULT_ADDR
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: addr
|
||||
NodeSelector: {}
|
||||
molgenis-it:
|
||||
InheritFrom: molgenis
|
||||
Label: molgenis-it
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
Containers:
|
||||
elasticsearch:
|
||||
Image: docker.elastic.co/elasticsearch/elasticsearch
|
||||
ImageTag: 5.5.3
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "1Gi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "1500Mi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: ES_JAVA_OPTS
|
||||
value: "-Xms512m -Xmx512m"
|
||||
- type: KeyValue
|
||||
key: cluster.name
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: bootstrap.memory_lock
|
||||
value: "true"
|
||||
- type: KeyValue
|
||||
key: xpack.security.enabled
|
||||
value: "false"
|
||||
- type: KeyValue
|
||||
key: discovery.type
|
||||
value: single-node
|
||||
postgres:
|
||||
Image: postgres
|
||||
ImageTag: 9.6-alpine
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "250Mi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "250Mi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: POSTGRES_USER
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: POSTGRES_PASSWORD
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: POSTGRES_DB
|
||||
value: molgenis
|
||||
opencpu:
|
||||
Image: molgenis/opencpu
|
||||
AlwaysPullImage: true
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "256Mi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "512Mi"
|
||||
NodeSelector: {}
|
||||
|
||||
#secret contains configuration for the kubernetes secrets that jenkins can access
|
||||
secret:
|
||||
# vault configures the vault secret
|
||||
vault:
|
||||
token: xxxx
|
||||
addr: "https://vault-operator.vault-operator.svc:8200"
|
||||
skipVerify: "1"
|
||||
# githubToken contains access token for jenkins bot account on github.com
|
||||
gitHub:
|
||||
user: "molgenis-jenkins"
|
||||
token: xxxx
|
||||
# gogs contains access token for jenkins bot account on RuG GoGs
|
||||
gogs:
|
||||
user: p281392
|
||||
token: xxxx
|
||||
# registry contains credentials for registry.molgenis.org
|
||||
registry:
|
||||
user: admin
|
||||
password: xxxx
|
||||
# dockerHubPassword contains password for hub.docker.com
|
||||
dockerHub:
|
||||
user: molgenisci
|
||||
password: xxxx
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
# Patterns to ignore when building packages.
|
||||
# This supports shell glob matching, relative path matching, and
|
||||
# negation (prefixed with !). Only one pattern per line.
|
||||
.DS_Store
|
||||
# Common VCS dirs
|
||||
.git/
|
||||
.gitignore
|
||||
.bzr/
|
||||
.bzrignore
|
||||
.hg/
|
||||
.hgignore
|
||||
.svn/
|
||||
# Common backup files
|
||||
*.swp
|
||||
*.bak
|
||||
*.tmp
|
||||
*~
|
||||
# Various IDEs
|
||||
.project
|
||||
.idea/
|
||||
*.tmproj
|
||||
|
|
@ -1,8 +0,0 @@
|
|||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: Nexus stack for MOLGENIS
|
||||
name: molgenis-nexus
|
||||
version: 0.4.2
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg
|
||||
|
|
@ -1,64 +0,0 @@
|
|||
# MOLGENIS - NEXUS Helm Chart
|
||||
|
||||
NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
|
||||
|
||||
## Chart Details
|
||||
|
||||
This chart will deploy:
|
||||
|
||||
- 1 NEXUS-nfs initialization container
|
||||
|
||||
We need this container to avoid permission issues on the NEXUS docker
|
||||
- 1 NEXUS container
|
||||
- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
|
||||
|
||||
## Backup restore
|
||||
There are two steps in restoring the NEXUS.
|
||||
|
||||
- Database
|
||||
- Blobstore
|
||||
|
||||
### Restore the database
|
||||
Go to the commandline:
|
||||
|
||||
```bash
|
||||
kubectl get pv
|
||||
```
|
||||
|
||||
```bash
|
||||
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
|
||||
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
|
||||
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
|
||||
| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
|
||||
```
|
||||
|
||||
The persistent volume is the one in the molgenis-nexus namespace.
|
||||
|
||||
Go to the NFS-provisioner to the path of the persistent volume:
|
||||
|
||||
```bash
|
||||
ls -t --full-time | head -7 | xargs cp ../restore-from-backup/
|
||||
```
|
||||
|
||||
### Restore the blobstore
|
||||
You can copy the directory ```blobs``` to the target persistent volume ```/ blobs```.
|
||||
|
||||
You can now bring the NEXUS back up.
|
||||
|
||||
## Installing the Chart
|
||||
|
||||
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.
|
||||
|
||||
|
||||
|
|
@ -1,551 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
|
||||
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" width="500px" height="264px" viewBox="0 0 500 264" enable-background="new 0 0 500 264" xml:space="preserve"> <image id="image0" width="500" height="264" x="0" y="0"
|
||||
xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAfQAAAEICAIAAAAm5JG/AAAABGdBTUEAALGPC/xhBQAAACBjSFJN
|
||||
AAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAABmJLR0QA/wD/AP+gvaeTAAAA
|
||||
CXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH4gQKFAE5UFTkaAAAeI5JREFUeNrtnXd8FMUXwGfb
|
||||
9bv0hHRSCQmkAUmA0BFEFJEmoAIWREVQlN5BBUQExIKKDVFEEFAQVBDkRw8ttEAgAUJ6b5dc3fL7
|
||||
Y+E4Llf2Su6SMN8Pn+OyO/t2du7u7ds3b95DGIYBEAgEAmlboK7uAAQCgUAcD1TuEAgE0gaByh0C
|
||||
gUDaIFC5QyAQSBsEKncIBAJpg0DlDoFAIG0QqNwhEAikDQKVOwQCgbRBoHKHQCCQNghU7hAIBNIG
|
||||
gcodAoFA2iBQuUMgEEgbBCp3CAQCaYNA5Q6BQCBtEKjcIRAIpA0ClTsEAoG0QaByh0AgkDYIVO4Q
|
||||
CATSBoHKHQKBQNogULlDIBBIGwQqdwgEAmmDQOUOgUAgbRCo3CEQCKQNApU7BAKBtEGgcodAIJA2
|
||||
CFTuEAgE0gbBXd0BSItmX3b1xoziehUlV1NKkmKYB7sQBIgInGEYAAAfRxAE+WBQ+/4R7q7ucuuG
|
||||
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|
||||
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|
||||
QP1uBQzDMAyDoujek9e++vNieW2jSkvRNPxhtlYQBBAYJhXxkiP91r7+GEBQBHGBAxwqd4gRJEtO
|
||||
NGoomw+/MC05KUDi6otoNVAURZLkpn0X1uw86yUVuLo7EIehpeggL8nm2U96yiQohjnZRQMnVCGG
|
||||
BK3MsEezAwCSP71Q2ah19XW0AhiGoWmapsiz1wu++fsS1OxtDAJDi6sbp312AMMxmqKdfHao3CEP
|
||||
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|
||||
OeUN2u/Olbr6alo6DMMwNLlxzwUGcWFUBaR5EfOJgxfyauWNULlDXMadapWWctgczJt7cl19QS0d
|
||||
hmGUSvXlvHIeBn+JbZmaelVVbQNFUc6c44RfKcg9SJqJ/+S8AwUqtc52MrY6KIpSabTVcjWKQru9
|
||||
LaMiqUalGip3iGtQaukG++ZRm/La7zmuvqwWDU3TNE1iCIAha20bFACGoSjKwb8viyeFQAAAoFrp
|
||||
+PiWb89Ct7sFMATxcxPAqPa2jZCP8Z3ueYPKHXKPknrHK3eSZhTQOWMWDEW7d/BWaZ1q00GcCc0w
|
||||
AR5CqYgH49whrkFNNosWzqlUuPrKWi4YhgEU6xnj1z3Sk3TcVDakRVGn0E7oFcrnERiGOfO8MHFY
|
||||
W4Nm1LdKPy6r30vRjQAAmSgpxv89IS/E4oFM8zh+ocoyA4IgBEFQKG9Sn7A7FVfrlCQKIyLbFhTN
|
||||
vDEgNCrIi+DxURRFUefZ01C5txHUZHlOyXv1yktaqh6ABzZ4vSLzzK2nMFQkE3YO8X7VXdTVlAQB
|
||||
3ixfu1B3vqvHpuWCoihBECKhsJ2P+7ynIj/442atkiYwqN/bAgwAdY3k5L7+jyWFIISQz+fjuFP1
|
||||
LVTubYHL+VPqFBdoxtTKUoaiG2saT9c0nnYTdkls/73RRl4iwuEdw1CkOcS2GVjLXSwWkyQZ4Kv9
|
||||
eHzcTycKsksaG9W0lr7/KAVVfSuCAQABKAKEBOoj5Y1JaRcb6iOQyCQSMY/Hc6bZDqBybwOcyumn
|
||||
Ias4Nq5Tns/IHRLtv9RDnGqwy1fCc3jfJDynOhlbHQiCoCjK4/GkUikAoJ7AJ/Th1cob6xvVapIE
|
||||
DANVe2uDQRAEQVCJkOchFUglUqFUKpPJhEIhjuNOnlCFyr11c/xGGkVbN2Op0hZdzp8cH/KVh7i7
|
||||
/nYR4Xiz4u8XO7l2fFo+CILgOC4QCFgrXigUiiUSX62WpmmKogBM2tq6QBAEQTAMwzBMKBQKhUKR
|
||||
SCQQCAiCcH5+CZjytxVz4mZPkpLbfHha1EE+7qe/ZV929ZObrzqqeygCqBW9XTg+rQg2PSRJkhqN
|
||||
RqvVkiRJ07STU5FAHAWr3AmC4PF4OI5jGOZkhwwLtNxbKxfvTrRHswMArhZM6xK2XX/L0BhPDEUo
|
||||
By2omdSlnQvHp3XBmnv3gmcoimEYJ69mhDgQFEV1HyiLS7oBlXurRE2W1yku2SmkQZVdqzjrLuqm
|
||||
v7FfuPu/uTUO6eSGpyJcNT6tFNa+c4mVB2l7wK9Rq+R60Vz9eEebqZQfNthy8OXOHXyE9kteMbi9
|
||||
GM6mQiCuAyr3VkmdwjGlMIqqf1ZrSww2Zr/TzSZhD0hv7zavr+VlUxAIpPmAyr310aC64UBpFfJD
|
||||
TTfumRBns8Bn432OTUlw/rBAIBB9YLRM6+NUzgANWeEoaQEeY6LaLWy6vbJRG7Qqw9qEM0NjPP+c
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qZcsWQIA6Ny5M0VR+tt1K48mTpx48eLF/Pz88vLynJycffv2DR48GEXRJUuWdO/eXSgUXr58Wf/A
|
||||
mTNnspmHp0yZkpGRUVpaWlNTU1NTU1BQ8Pvvv3fo0AEAMGjQILVa7eoPysFA5Q6BtHHGjRsHAJg5
|
||||
cyb3Q65fv85GPZq5JVy4cCEsLIxVuN7e3sHBwYGBge7u7uyWmTNnlpWV6bevq6vr2LEjAOCTTz4x
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
MDE6MDB0d1BTAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE4LTA0LTEwVDIxOjAyOjE5KzAxOjAwBSro
|
||||
7wAAAABJRU5ErkJggg==" />
|
||||
</svg>
|
||||
|
Before Width: | Height: | Size: 42 KiB |
|
|
@ -1,32 +0,0 @@
|
|||
{{/* vim: set filetype=mustache: */}}
|
||||
{{/*
|
||||
Expand the name of the chart.
|
||||
*/}}
|
||||
{{- define "nexus.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 "nexus.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 "nexus.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
|
@ -1,65 +0,0 @@
|
|||
apiVersion: extensions/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
creationTimestamp: null
|
||||
name: {{ .Values.nexus.name }}
|
||||
labels:
|
||||
app: {{ .Values.nexus.name }}
|
||||
environment: {{ .Values.environment }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
strategy:
|
||||
type: {{ .Values.nexus.strategy.type }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ .Values.nexus.selector }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ .Values.nexus.name }}
|
||||
creationTimestamp: null
|
||||
spec:
|
||||
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
||||
initContainers:
|
||||
- name: nexus-nfs
|
||||
image: busybox
|
||||
command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
|
||||
volumeMounts:
|
||||
- name: molgenis-nexus-nfs
|
||||
mountPath: "/nexus-data"
|
||||
containers:
|
||||
- name: {{ .Values.nexus.name }}
|
||||
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
||||
imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
|
||||
ports:
|
||||
- containerPort: {{ .Values.nexus.port.ui }}
|
||||
- containerPort: {{ .Values.nexus.port.docker }}
|
||||
volumeMounts:
|
||||
- name: molgenis-nexus-nfs
|
||||
mountPath: /nexus-data
|
||||
livenessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.nexus.port.ui }}
|
||||
initialDelaySeconds: 120
|
||||
periodSeconds: 20
|
||||
failureThreshold: 15
|
||||
successThreshold: 1
|
||||
readinessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.nexus.port.ui }}
|
||||
initialDelaySeconds: 120
|
||||
periodSeconds: 20
|
||||
failureThreshold: 15
|
||||
successThreshold: 1
|
||||
|
||||
volumes:
|
||||
- name: molgenis-nexus-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.persistence.claim }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
|
|
@ -1,55 +0,0 @@
|
|||
apiVersion: extensions/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
creationTimestamp: null
|
||||
name: {{ .Values.nexusProxy.name }}
|
||||
labels:
|
||||
app: {{ .Values.nexusProxy.name }}
|
||||
environment: {{ .Values.environment }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
strategy:
|
||||
type: {{ .Values.nexusProxy.strategy.type }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ .Values.nexusProxy.selector }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ .Values.nexusProxy.name }}
|
||||
creationTimestamp: null
|
||||
spec:
|
||||
restartPolicy: {{ .Values.nexusProxy.restartPolicy }}
|
||||
containers:
|
||||
- name: {{ .Values.nexusProxy.name }}
|
||||
image: "{{ .Values.nexusProxy.image.repository }}:{{ .Values.nexusProxy.image.tag }}"
|
||||
imagePullPolicy: {{ .Values.nexusProxy.image.pullPolicy }}
|
||||
env:
|
||||
- name: PROXY_SERVICE
|
||||
value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
|
||||
- name: SERVER_NAME
|
||||
value: {{ .Values.nexusProxy.hostname }}
|
||||
ports:
|
||||
- containerPort: {{ .Values.nexusProxy.port }}
|
||||
resources: {}
|
||||
livenessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.nexusProxy.port }}
|
||||
initialDelaySeconds: 1500
|
||||
periodSeconds: 20
|
||||
failureThreshold: 5
|
||||
successThreshold: 1
|
||||
readinessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.nexusProxy.port }}
|
||||
initialDelaySeconds: 150
|
||||
periodSeconds: 20
|
||||
failureThreshold: 15
|
||||
successThreshold: 1
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
|
|
@ -1,38 +0,0 @@
|
|||
{{- if .Values.ingress.enabled }}
|
||||
{{- range .Values.ingress.hosts }}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
labels:
|
||||
app: {{ $.Values.nexusProxy.name }}
|
||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
||||
release: "{{ $.Release.Name }}"
|
||||
heritage: "{{ $.Release.Service }}"
|
||||
annotations:
|
||||
kubernetes.io/ingress.class: "nginx"
|
||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||
{{- 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: {{ $.Values.nexusProxy.name }}
|
||||
servicePort: {{ $.Values.nexusProxy.port }}
|
||||
{{- if .tls }}
|
||||
tls:
|
||||
- hosts:
|
||||
- {{ .name }}
|
||||
secretName: {{ .tlsSecret }}
|
||||
{{- end }}
|
||||
---
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
{{- if .Values.persistence.enabled -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.persistence.claim }}
|
||||
annotations:
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
||||
spec:
|
||||
accessModes:
|
||||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.persistence.size }}
|
||||
{{- end }}
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ .Values.nexus.name }}
|
||||
labels:
|
||||
app: {{ .Values.nexus.name }}
|
||||
spec:
|
||||
type: {{ .Values.nexus.service.type }}
|
||||
ports:
|
||||
- name: ui
|
||||
port: {{ .Values.nexus.port.ui }}
|
||||
- name: docker
|
||||
port: {{ .Values.nexus.port.docker }}
|
||||
selector:
|
||||
app: {{ .Values.nexus.selector }}
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ .Values.nexusProxy.name }}
|
||||
labels:
|
||||
app: {{ .Values.nexusProxy.name }}
|
||||
spec:
|
||||
type: {{ .Values.nexusProxy.service.type }}
|
||||
ports:
|
||||
- name: {{ .Values.nexusProxy.name }}
|
||||
port: {{ .Values.nexusProxy.port }}
|
||||
selector:
|
||||
app: {{ .Values.nexusProxy.selector }}
|
||||
|
|
@ -1,65 +0,0 @@
|
|||
# Default values for nexus.
|
||||
# This is a YAML-formatted file.
|
||||
# Declare variables to be passed into your templates.
|
||||
|
||||
replicaCount: 1
|
||||
|
||||
environment: production
|
||||
|
||||
nexus:
|
||||
name: nexus
|
||||
strategy:
|
||||
type: Recreate
|
||||
selector: nexus
|
||||
restartPolicy: Always
|
||||
image:
|
||||
repository: molgenis/nexus3
|
||||
tag: latest
|
||||
pullPolicy: Always
|
||||
port:
|
||||
docker: 5000
|
||||
ui: 8081
|
||||
path:
|
||||
dockerV2: v2
|
||||
service:
|
||||
type: ClusterIP
|
||||
|
||||
nexusProxy:
|
||||
name: nexus-proxy
|
||||
hostname: registry.molgenis.org
|
||||
strategy:
|
||||
type: Recreate
|
||||
selector: nexus-proxy
|
||||
restartPolicy: Always
|
||||
image:
|
||||
repository: molgenis/httpd
|
||||
tag: latest
|
||||
pullPolicy: Always
|
||||
port: 80
|
||||
service:
|
||||
type: LoadBalancer
|
||||
|
||||
|
||||
ingress:
|
||||
enabled: true
|
||||
annotations: {}
|
||||
path: /
|
||||
hosts:
|
||||
- name: registry.molgenis.org
|
||||
tls: []
|
||||
|
||||
persistence:
|
||||
enabled: true
|
||||
claim: molgenis-nexus
|
||||
size: 500Gi
|
||||
|
||||
|
||||
resources: {}
|
||||
|
||||
nodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
# Patterns to ignore when building packages.
|
||||
# This supports shell glob matching, relative path matching, and
|
||||
# negation (prefixed with !). Only one pattern per line.
|
||||
.DS_Store
|
||||
# Common VCS dirs
|
||||
.git/
|
||||
.gitignore
|
||||
.bzr/
|
||||
.bzrignore
|
||||
.hg/
|
||||
.hgignore
|
||||
.svn/
|
||||
# Common backup files
|
||||
*.swp
|
||||
*.bak
|
||||
*.tmp
|
||||
*~
|
||||
# Various IDEs
|
||||
.project
|
||||
.idea/
|
||||
*.tmproj
|
||||
|
|
@ -1,8 +0,0 @@
|
|||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: Opencpu stack for MOLGENIS
|
||||
name: molgenis-opencpu
|
||||
version: 0.1.1
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-opencpu/catalogIcon-molgenis-opencpu.svg
|
||||
|
|
@ -1,38 +0,0 @@
|
|||
# MOLGENIS - OpenCPU Helm Chart
|
||||
|
||||
NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
|
||||
|
||||
## Containers
|
||||
|
||||
This chart will deploy the following containers:
|
||||
|
||||
- OpenCPU
|
||||
- MOLGENIS-httpd (to proxy the registry and docker to one domain)
|
||||
|
||||
## Provisioning
|
||||
You can choose for the OpenCPU 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.
|
||||
|
||||
- ```opencpu.image.repository```
|
||||
- ```opencpu.image.tag```
|
||||
|
||||
You can do this in the questions in Rancher or in the ```values.yaml```.
|
||||
|
||||
|
||||
|
||||
## 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.
|
||||
|
||||
|
||||
File diff suppressed because one or more lines are too long
|
Before Width: | Height: | Size: 245 KiB |
|
|
@ -1,28 +0,0 @@
|
|||
|
||||
categories:
|
||||
- MOLGENIS
|
||||
questions:
|
||||
- variable: ingress.enabled
|
||||
label: Enable ingress
|
||||
default: false
|
||||
description: "Enable ingress"
|
||||
type: boolean
|
||||
required: true
|
||||
group: "Load balancing"
|
||||
- variable: opencpu.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: opencpu.image.tag
|
||||
label: Version
|
||||
default: ""
|
||||
description: "Select a OpenCPU 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 "opencpu.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 "opencpu.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 "opencpu.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
|
@ -1,35 +0,0 @@
|
|||
apiVersion: extensions/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
{{- with .Values.ingress.annotations }}
|
||||
annotations:
|
||||
{{ toYaml . | indent 4 }}
|
||||
{{- end }}
|
||||
name: {{ template "opencpu.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "opencpu.name" . }}
|
||||
chart: {{ template "opencpu.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ template "opencpu.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ template "opencpu.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
spec:
|
||||
containers:
|
||||
{{- with .Values.opencpu }}
|
||||
- name: {{ .name }}
|
||||
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
ports:
|
||||
- containerPort: {{ .service.port }}
|
||||
{{- 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: {{ $.Values.opencpu.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: {{ $.Values.opencpu.service.name }}
|
||||
servicePort: {{ $.Values.opencpu.service.port }}
|
||||
{{- if .tls }}
|
||||
tls:
|
||||
- hosts:
|
||||
- {{ .name }}
|
||||
secretName: {{ .tlsSecret }}
|
||||
{{- end }}
|
||||
---
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ .Values.opencpu.service.name }}
|
||||
labels:
|
||||
app: {{ .Values.opencpu.service.name }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
type: {{ .Values.opencpu.service.type }}
|
||||
loadBalancerSourceRanges:
|
||||
{{- range $index, $rule := .Values.opencpu.service.firewall }}
|
||||
- {{ $rule }}
|
||||
{{- end }}
|
||||
ports:
|
||||
- name: {{ .Values.opencpu.service.name }}
|
||||
port: {{ .Values.opencpu.service.port }}
|
||||
selector:
|
||||
app: {{ template "opencpu.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
|
|
@ -1,41 +0,0 @@
|
|||
# Default values for nexus.
|
||||
# This is a YAML-formatted file.
|
||||
# Declare variables to be passed into your templates.
|
||||
|
||||
replicaCount: 1
|
||||
|
||||
environment: production
|
||||
|
||||
opencpu:
|
||||
name: opencpu
|
||||
strategy:
|
||||
type: Recreate
|
||||
restartPolicy: Always
|
||||
image:
|
||||
repository: registry.hub.docker.com
|
||||
name: molgenis/opencpu
|
||||
tag: stable
|
||||
pullPolicy: Always
|
||||
service:
|
||||
name: opencpu
|
||||
type: LoadBalancer
|
||||
port: 8004
|
||||
firewall:
|
||||
- 145.100.224.1/24
|
||||
|
||||
ingress:
|
||||
enabled: false
|
||||
annotations: {
|
||||
kubernetes.io/ingress.class: "nginx",
|
||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||
}
|
||||
path: /
|
||||
hosts:
|
||||
- name: opencpu.molgenis.org
|
||||
tls: []
|
||||
|
||||
nodeSelector: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
# Patterns to ignore when building packages.
|
||||
# This supports shell glob matching, relative path matching, and
|
||||
# negation (prefixed with !). Only one pattern per line.
|
||||
.DS_Store
|
||||
# Common VCS dirs
|
||||
.git/
|
||||
.gitignore
|
||||
.bzr/
|
||||
.bzrignore
|
||||
.hg/
|
||||
.hgignore
|
||||
.svn/
|
||||
# Common backup files
|
||||
*.swp
|
||||
*.bak
|
||||
*.tmp
|
||||
*~
|
||||
# Various IDEs
|
||||
.project
|
||||
.idea/
|
||||
*.tmproj
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS vault
|
||||
name: molgenis-vault
|
||||
version: 0.1.1
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg
|
||||
|
|
@ -1,52 +0,0 @@
|
|||
# MOLGENIS Vault helm chart
|
||||
|
||||
This chart creates a vault operator, but NO vault.
|
||||
The vault operator defines a new custom resource named `vault` that you can use to create vaults.
|
||||
|
||||
After launching the operator, create the molgenis vault manually:
|
||||
`kubectl create -f resources/vault.yaml`
|
||||
|
||||
That creates a new vault with two vault pods.
|
||||
|
||||
See https://github.com/coreos/vault-operator/blob/master/doc/user/vault.md
|
||||
|
||||
## Parameters
|
||||
|
||||
### Azure cloud credentials
|
||||
Define credentials for backup to the Azure Blob Store.
|
||||
See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/abs_backup.md).
|
||||
|
||||
| Parameter | Description | Default |
|
||||
| --------------- | ----------------------------- | ------------------ |
|
||||
| `abs.account` | name of storage account | `fdlkops` |
|
||||
| `abs.accessKey` | access key of storage account | `xxxx` |
|
||||
| `abs.cloud` | name of cloud environment | `AzurePublicCloud` |
|
||||
|
||||
### Backup job
|
||||
Define the schedule of the backup job
|
||||
|
||||
| Parameter | Description | Default |
|
||||
| -------------------- | ---------------------------- | ------------- |
|
||||
| `backupJob.enable` | Enable backup cronjob | `true` |
|
||||
| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1` |
|
||||
|
||||
### UI
|
||||
|
||||
Parameter | Description | Default
|
||||
--------- | ----------- | -------
|
||||
`ui.replicaCount` | desired number of Vault UI pod | `1`
|
||||
`ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui`
|
||||
`ui.image.tag` | Vault UI container image tag | `latest`
|
||||
`ui.resources` | Vault UI pod resource requests & limits | `{}`
|
||||
`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}`
|
||||
`ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true`
|
||||
`ui.ingress.annotations` | Vault UI Ingress annotations | `{}`
|
||||
`ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org`
|
||||
`ui.ingress.tls` | Vault UI Ingress TLS configuration (YAML) | `[]`
|
||||
`ui.vault.url` | Vault UI default vault url | `https://vault.vault-operator:8200`
|
||||
`ui.vault.auth` | Vault UI login method | `GITHUB`
|
||||
`ui.service.name` | Vault UI service name | `vault-ui`
|
||||
`ui.service.type` | type of ui service to create | `ClusterIP`
|
||||
`ui.service.externalPort` | Vault UI service target port | `8000`
|
||||
`ui.service.internalPort` | Vault UI container port | `8000`
|
||||
`ui.service.nodePort` | Port to be used as the service NodePort (ignored if `server.service.type` is not `NodePort`) | `0`
|
||||
|
|
@ -1,627 +0,0 @@
|
|||
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12xl56300JnuOwv2hvzx9pYrHiLYalrFifjsDh6JVFniySQnnDOZynTsGRvDnG0EYhhnb6wMDmZP
|
||||
ATn7sAt57do1fb17964k1wQk2ty5c9XOPXV+PXC2sg52kuhgxkHYz8LDfk6QCWD8ZCdjh8TOmGy5
|
||||
4lGQiK+t1DFPvBPeLKbiyNhmMRlPAiJpZ13aQ2ch/8lSW1v2ogiVzI4FZsdptrJ/1pmOPeyg2IN/
|
||||
eWXLFd8s0T6+WaJ9PAS7w7Qn4j0yGW6ZeJYlAz0jwVQMZ1MMc5aR0SHMeujn7A0lmFe8JwiJxTqs
|
||||
ix7sCG3lXtmOYzsF67vf6Mce4ur2wkdMJuK/34hiZ/BAEmgCDzH/euK9smKYwHqg82Iq1DOadioa
|
||||
zLpuF4RSOWAnmMqLVWrRftYP7YDYh/34h//sTN5Of0i2XPEYhAExnIivvfoftcSTUVQMGRrKYCrK
|
||||
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|
||||
PyukoUT45cRDOBVDZZGBMczZy3ywz4/1Mx57ikrWKWq3EwLGL/cjhrGH+b4e/diLzOt/4YpHAQ6g
|
||||
2A0KYRxiPtjHx/oZjz1FJevE/MBOtwtiODLAofE+3zH2MN/Xox97kXn9b5n4vIrSuGpFIBFfLT5K
|
||||
syYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqz
|
||||
JhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMm
|
||||
EV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrPmL/hk6fsEzapeAAAAAElF
|
||||
TkSuQmCC
|
||||
"
|
||||
style="image-rendering:optimizeQuality"
|
||||
preserveAspectRatio="none"
|
||||
height="94.666664"
|
||||
width="84" /><g
|
||||
inkscape:groupmode="layer"
|
||||
id="layer1"
|
||||
inkscape:label="base"
|
||||
style="opacity:1" /></svg>
|
||||
|
Before Width: | Height: | Size: 46 KiB |
Binary file not shown.
Binary file not shown.
|
|
@ -1,9 +0,0 @@
|
|||
dependencies:
|
||||
- name: vault-operator
|
||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||
version: 0.1.1
|
||||
- name: etcd-operator
|
||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||
version: 0.8.0
|
||||
digest: sha256:47aa645df7dfce9760905800321599de05995ae50090735d45310936dbaa46de
|
||||
generated: 2018-09-06T18:59:39.861922543+02:00
|
||||
|
|
@ -1,7 +0,0 @@
|
|||
dependencies:
|
||||
- name: vault-operator
|
||||
version: ^0.1.1
|
||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||
- name: etcd-operator
|
||||
version: ^0.8.0
|
||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
# Use kubectl create -f restore.yaml to manually execute a restore of the vault
|
||||
apiVersion: "etcd.database.coreos.com/v1beta2"
|
||||
kind: "EtcdRestore"
|
||||
metadata:
|
||||
# The restore CR name must be the same as spec.etcdCluster.name
|
||||
name: vault-etcd
|
||||
namespace: vault-operator
|
||||
spec:
|
||||
etcdCluster:
|
||||
# The namespace is the same as this EtcdRestore CR
|
||||
name: vault-etcd
|
||||
backupStorageType: ABS
|
||||
abs:
|
||||
path: vault/backup-<specify the backup name>
|
||||
absSecret: abs
|
||||
|
|
@ -1,9 +0,0 @@
|
|||
# Use kubectl create -f vault.yaml to manually create a vault
|
||||
apiVersion: "vault.security.coreos.com/v1alpha1"
|
||||
kind: "VaultService"
|
||||
metadata:
|
||||
name: "vault"
|
||||
namespace: "vault-operator"
|
||||
spec:
|
||||
nodes: 2
|
||||
version: "0.9.1-0"
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
Vault operator created
|
||||
|
||||
Next steps:
|
||||
|
||||
* Manually create a vault using resources/vault.yaml
|
||||
* Manually restore a backup using resources/backup.yaml
|
||||
* Unseal the vault pods
|
||||
|
||||
{{ if .Values.backupJob.enable }}
|
||||
!! Make sure to check if the backups succeed !!
|
||||
{{ else }}
|
||||
!!!!!! NO BACKUPS CONFIGURED !!!!!!
|
||||
{{ end }}
|
||||
|
|
@ -1,54 +0,0 @@
|
|||
{{/*
|
||||
Define vault ui fullname
|
||||
*/}}
|
||||
{{- define "vault.ui.fullname" -}}
|
||||
{{- printf "%s-ui" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
Define vault service url for the ui
|
||||
*/}}
|
||||
{{- define "vault.service.url" -}}
|
||||
{{- printf "https://%s:8200" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/* See https://github.com/helm/helm/issues/4535 */}}
|
||||
{{- define "call-nested" }}
|
||||
{{- $dot := index . 0 }}
|
||||
{{- $subchart := index . 1 }}
|
||||
{{- $template := index . 2 }}
|
||||
{{- include $template (dict "Chart" (dict "Name" $subchart) "Values" (index $dot.Values $subchart) "Release" $dot.Release "Capabilities" $dot.Capabilities) }}
|
||||
{{- end }}
|
||||
|
||||
{{/* vim: set filetype=mustache: */}}
|
||||
{{/*
|
||||
Expand the name of the chart.
|
||||
*/}}
|
||||
{{- define "molgenis-vault.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 "molgenis-vault.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 $name | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
Create chart name and version as used by the chart label.
|
||||
*/}}
|
||||
{{- define "molgenis-vault.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
# Secret to access microsoft azure blob store
|
||||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
name: abs
|
||||
type: Opaque
|
||||
stringData:
|
||||
storage-account: {{ .Values.abs.account }}
|
||||
storage-key: {{ .Values.abs.accessKey }}
|
||||
cloud: {{ .Values.abs.cloud }}
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
# configmap to use as a template by the backup cronjob to create etcdbackup instances
|
||||
apiVersion: v1
|
||||
kind: ConfigMap
|
||||
metadata:
|
||||
name: backup-config
|
||||
data:
|
||||
backup_cr.yaml: |
|
||||
apiVersion: "etcd.database.coreos.com/v1beta2"
|
||||
kind: "EtcdBackup"
|
||||
metadata:
|
||||
generateName: vault-backup-
|
||||
spec:
|
||||
etcdEndpoints: ["https://vault-etcd-client:2379"]
|
||||
storageType: ABS
|
||||
clientTLSSecret: vault-etcd-client-tls
|
||||
abs:
|
||||
path: vault/backup.<NOW>
|
||||
absSecret: abs
|
||||
|
|
@ -1,30 +0,0 @@
|
|||
{{- if .Values.backupJob.enable }}
|
||||
# cronjob that creates etcdbackups using the etcd backup serviceaccount
|
||||
apiVersion: batch/v1beta1
|
||||
kind: CronJob
|
||||
metadata:
|
||||
name: etcd-backup
|
||||
spec:
|
||||
schedule: {{ .Values.backupJob.schedule | quote }}
|
||||
jobTemplate:
|
||||
spec:
|
||||
template:
|
||||
spec:
|
||||
serviceAccountName: {{ include "call-nested" (list . "etcd-operator" "etcd-operator.serviceAccountName") }}
|
||||
containers:
|
||||
- name: etcd-backup
|
||||
image: lachlanevenson/k8s-kubectl
|
||||
command:
|
||||
- /bin/sh
|
||||
- "-ec"
|
||||
- |
|
||||
sed -e "s|<NOW>|$(date '+%Y-%m-%d_%H:%M:%S')|g" /var/etcd_backup/backup_cr.yaml | kubectl create -f -
|
||||
volumeMounts:
|
||||
- name: backup-config
|
||||
mountPath: /var/etcd_backup
|
||||
restartPolicy: OnFailure
|
||||
volumes:
|
||||
- name: backup-config
|
||||
configMap:
|
||||
name: backup-config
|
||||
{{- end }}
|
||||
|
|
@ -1,30 +0,0 @@
|
|||
{{- if .Values.ui.ingress.enabled -}}
|
||||
{{- $serviceName := include "vault.ui.fullname" . -}}
|
||||
{{- $servicePort := .Values.ui.service.externalPort -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: {{ template "vault.ui.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "molgenis-vault.name" . }}
|
||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
annotations:
|
||||
{{- range $key, $value := .Values.ui.ingress.annotations }}
|
||||
{{ $key }}: {{ $value | quote }}
|
||||
{{- end }}
|
||||
spec:
|
||||
rules:
|
||||
- host: {{ .Values.ui.ingress.host }}
|
||||
http:
|
||||
paths:
|
||||
- path:
|
||||
backend:
|
||||
serviceName: {{ $serviceName }}
|
||||
servicePort: {{ $servicePort }}
|
||||
{{- if .Values.ui.ingress.tls }}
|
||||
tls:
|
||||
{{ toYaml .Values.ui.ingress.tls | indent 4 }}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
|
|
@ -1,23 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ template "vault.ui.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "vault-operator.name" . }}
|
||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
type: {{ .Values.ui.service.type }}
|
||||
ports:
|
||||
- port: {{ .Values.ui.service.externalPort }}
|
||||
targetPort: {{ .Values.ui.service.internalPort }}
|
||||
protocol: TCP
|
||||
name: {{ .Values.ui.service.name }}
|
||||
{{- if .Values.ui.service.nodePort }}
|
||||
nodePort: {{ .Values.ui.service.nodePort }}
|
||||
{{- end }}
|
||||
selector:
|
||||
app: {{ template "vault-operator.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
component: {{ .Values.ui.name }}
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
apiVersion: apps/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
name: {{ template "vault.ui.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "vault-operator.name" . }}
|
||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
component: {{ .Values.ui.name }}
|
||||
spec:
|
||||
replicas: {{ .Values.ui.replicaCount }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ template "vault-operator.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
component: {{ .Values.ui.name }}
|
||||
spec:
|
||||
containers:
|
||||
- name: {{ .Values.ui.name }}
|
||||
image: "{{ .Values.ui.image.repository }}:{{ .Values.ui.image.tag }}"
|
||||
imagePullPolicy: {{ .Values.imagePullPolicy }}
|
||||
env:
|
||||
- name: VAULT_URL_DEFAULT
|
||||
{{- if .Values.ui.vault.url }}
|
||||
value: {{ .Values.ui.vault.url }}
|
||||
{{ else }}
|
||||
value: {{ template "vault.service.url" . }}
|
||||
{{- end }}
|
||||
- name: VAULT_AUTH_DEFAULT
|
||||
value: {{ .Values.ui.vault.auth }}
|
||||
- name: NODE_TLS_REJECT_UNAUTHORIZED
|
||||
value: '0'
|
||||
ports:
|
||||
- containerPort: {{ .Values.ui.service.internalPort }}
|
||||
livenessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.ui.service.internalPort }}
|
||||
readinessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: {{ .Values.ui.service.internalPort }}
|
||||
resources:
|
||||
{{ toYaml .Values.ui.resources | indent 12 }}
|
||||
{{- if .Values.ui.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml .Values.ui.nodeSelector | indent 8 }}
|
||||
{{- end }}
|
||||
|
|
@ -1,79 +0,0 @@
|
|||
# Default values for molgenis-vault.
|
||||
# This is a YAML-formatted file.
|
||||
# Declare variables to be passed into your templates.
|
||||
|
||||
# abs gives details of the credentials to reach the azure backup storage
|
||||
abs:
|
||||
# account is the name of the Storage account
|
||||
account: fdlkops
|
||||
# access key for the Storage account
|
||||
accessKey: xxxx
|
||||
# default cloud
|
||||
cloud: AzurePublicCloud
|
||||
|
||||
# backupjob describes the backup cronjob
|
||||
backupJob:
|
||||
# enable enables the backup job
|
||||
enable: true
|
||||
# schedule gives the cron schedule for the backup job
|
||||
schedule: "0 12 * * 1"
|
||||
|
||||
###
|
||||
# All of the config variables related to setting up the etcd-operator
|
||||
# If you want more information about the variables exposed, please visit:
|
||||
# https://github.com/kubernetes/charts/tree/master/stable/etcd-operator#configuration
|
||||
###
|
||||
etcd-operator:
|
||||
deployments:
|
||||
etcdOperator: true
|
||||
backupOperator: true
|
||||
restoreOperator: true
|
||||
serviceAccount:
|
||||
etcdOperatorServiceAccount:
|
||||
create: true
|
||||
backupOperatorServiceAccount:
|
||||
create: true
|
||||
restoreOperatorServiceAccount:
|
||||
create: true
|
||||
etcdOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
backupOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
restoreOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
|
||||
ui:
|
||||
name: "vault-ui"
|
||||
replicaCount: 1
|
||||
image:
|
||||
repository: djenriquez/vault-ui
|
||||
tag: latest
|
||||
service:
|
||||
name: vault-ui
|
||||
type: ClusterIP
|
||||
externalPort: 8000
|
||||
internalPort: 8000
|
||||
# nodePort: 32001
|
||||
ingress:
|
||||
enabled: true
|
||||
# Used to create Ingress record (should used with service.type: ClusterIP).
|
||||
host: vault.molgenis.org
|
||||
|
||||
resources: {}
|
||||
# We usually recommend not to specify default resources and to leave this as a conscious
|
||||
# choice for the user. This also increases chances charts run on environments with little
|
||||
# resources, such as Minikube. If you do want to specify resources, uncomment the following
|
||||
# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
|
||||
# limits:
|
||||
# cpu: 100m
|
||||
# memory: 128Mi
|
||||
#requests:
|
||||
# cpu: 100m
|
||||
# memory: 128Mi
|
||||
nodeSelector: {}
|
||||
vault:
|
||||
auth: GITHUB
|
||||
url: https://vault.vault-operator:8200
|
||||
|
|
@ -1,8 +0,0 @@
|
|||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS - helm stack (in BETA)
|
||||
name: molgenis
|
||||
version: 0.4.3
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||
|
|
@ -1,138 +0,0 @@
|
|||
# MOLGENIS
|
||||
This chart is used for acceptance and production use cases.
|
||||
|
||||
## Containers
|
||||
This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
|
||||
|
||||
- MOLGENIS
|
||||
- ElasticSearch
|
||||
- PostgreSQL **(optional)**
|
||||
|
||||
## Provisioning
|
||||
You can choose from which registry you want to pull. There are 2 registries:
|
||||
- https://registry.molgenis.org
|
||||
- https://hub.docker.com
|
||||
|
||||
The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
|
||||
|
||||
The three properties you need to specify are:
|
||||
- ```molgenis.image.repository```
|
||||
- ```molgenis.image.name```
|
||||
- ```molgenis.image.tag```
|
||||
|
||||
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
||||
- ```molgenis.adminPassword```
|
||||
|
||||
### Firewall
|
||||
Is defined at service level you can specify this attribute in the values:
|
||||
|
||||
- ```molgenis.firewall.enabled``` default 'false'
|
||||
|
||||
If set to 'true' the following options are available. One of the options below has to be set.
|
||||
|
||||
- ```molgenis.firewall.umcg.enabled``` default 'false'
|
||||
- ```molgenis.firewall.cluster.enabled``` default 'false'
|
||||
|
||||
UMCG = only available within the UMCG.
|
||||
Cluster = only available within the GCC cluster environment.
|
||||
|
||||
## Services
|
||||
When you start MOLGENIS you need:
|
||||
- an elasticsearch instance (5.5.6)
|
||||
- an postgres instance (9.6)
|
||||
|
||||
You can attach additional services like:
|
||||
- an opencpu instance
|
||||
|
||||
### Elasticsearch
|
||||
You can configure elasticsearch by giving in the cluster location.
|
||||
|
||||
To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch.
|
||||
From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
|
||||
- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
|
||||
|
||||
To configure the index on a Elasticsearch cluster you can specify the clusterName property.
|
||||
- ```molgenis.services.elasticsearch.clusterName: molgenis```
|
||||
|
||||
### Postgres
|
||||
You can specify the location of the postgres instance by specify the following property:
|
||||
- ```molgenis.services.postgres.host: localhost```
|
||||
|
||||
You can specify the schema by filling out this property:
|
||||
- ```molgenis.services.postgres.scheme: molgenis```
|
||||
|
||||
You can specify credentials for the database scheme by specifying the following properties:
|
||||
- ```molgenis.services.postgres.user: molgenis```
|
||||
- ```molgenis.services.postgres.password: molgenis```
|
||||
|
||||
To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
|
||||
|
||||
```bash
|
||||
# answers for postgresql chart
|
||||
postgresUser=molgenis
|
||||
postgresPassword=molgenis
|
||||
postgresDatabase=molgenis
|
||||
persistence.enabled=false
|
||||
```
|
||||
|
||||
### OpenCPU
|
||||
You can specify the location of the OpenCPU cluster by specifying this property:
|
||||
- ```molgenis.services.opencpu.host: localhost```
|
||||
|
||||
You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
|
||||
|
||||
## Resources
|
||||
You can specify resources by resource type. There are 2 resource types.
|
||||
- memory of container
|
||||
- maximum heap space JVM
|
||||
|
||||
Specify memory usage of container:
|
||||
- ```molgenis.resources.limits.memory```
|
||||
|
||||
Specify memory usage for Java JVM:
|
||||
- ```molgenis.javaOpts.maxHeapSpace```
|
||||
|
||||
Select the resources you need dependant on the customer you need to serve.
|
||||
|
||||
## Persistence
|
||||
You can enable persistence on your MOLGENIS stack by specifying the following property.
|
||||
|
||||
- ```persistence.enabled``` default 'true'
|
||||
|
||||
You can also choose to retain the volume of the NFS.
|
||||
- ```persistence.retain``` default 'false'
|
||||
|
||||
The size and claim name can be specified per service. There are now two services that can be persist.
|
||||
|
||||
- MOLGENIS
|
||||
- ElasticSearch
|
||||
- PostgreSQL **(optional)**
|
||||
|
||||
MOLGENIS persistent properties.
|
||||
- ```molgenis.persistence.claim```
|
||||
- ```molgenis.persistence.size```
|
||||
|
||||
ElasticSearch persistent properties.
|
||||
- ```elasticsearch.persistence.claim```
|
||||
- ```elasticsearch.persistence.size```
|
||||
|
||||
PostgreSQL persistent properties.
|
||||
- ```postgres.persistence.claim```
|
||||
- ```postgres.persistence.size```
|
||||
|
||||
### Resolve you persistent volume
|
||||
You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
|
||||
|
||||
```
|
||||
kubectl get pv
|
||||
```
|
||||
|
||||
You can now view the persistent volume claims and the attached volumes.
|
||||
|
||||
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
|
||||
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
|
||||
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
|
||||
| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
|
||||
|
||||
You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
||||
When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
||||
File diff suppressed because it is too large
Load Diff
|
Before Width: | Height: | Size: 77 KiB |
|
|
@ -1,167 +0,0 @@
|
|||
|
||||
categories:
|
||||
- MOLGENIS
|
||||
questions:
|
||||
- variable: ingress.hosts[0].name
|
||||
label: Hostname
|
||||
default: "test.molgenis.org"
|
||||
description: "Hostname for your stack"
|
||||
type: hostname
|
||||
required: true
|
||||
group: "Load balancing"
|
||||
- variable: molgenis.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: molgenis.image.tag
|
||||
label: Version
|
||||
default: ""
|
||||
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
|
||||
type: string
|
||||
required: true
|
||||
group: "Provisioning"
|
||||
- variable: molgenis.adminPassword
|
||||
label: Administrator password
|
||||
default: ""
|
||||
description: "Enter an administrator password"
|
||||
type: password
|
||||
required: true
|
||||
group: "Provisioning"
|
||||
- variable: service.firewall.enabled
|
||||
label: Firewall enabled
|
||||
default: false
|
||||
description: "Firewall enabled (can be cluster or UMCG scoped)"
|
||||
type: boolean
|
||||
required: true
|
||||
group: "Provisioning"
|
||||
show_subquestion_if: true
|
||||
subquestions:
|
||||
- variable: service.firewall.kind
|
||||
default: "umcg"
|
||||
description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
|
||||
type: enum
|
||||
required: true
|
||||
options:
|
||||
- umcg
|
||||
- cluster
|
||||
label: Firewall kind
|
||||
- variable: molgenis.services.opencpu.host
|
||||
label: OpenCPU cluster
|
||||
default: "localhost"
|
||||
description: "Specify the OpenCPU cluster"
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.services.postgres.embedded
|
||||
label: Postgres embedded
|
||||
default: false
|
||||
description: "Do you want an embedded postgres"
|
||||
type: boolean
|
||||
required: true
|
||||
group: "Services"
|
||||
show_subquestion_if: false
|
||||
subquestions:
|
||||
- variable: molgenis.services.postgres.host
|
||||
label: Postgres cluster location
|
||||
default: ""
|
||||
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)"
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.services.postgres.scheme
|
||||
label: Database scheme
|
||||
default: "molgenis"
|
||||
description: "Set the database scheme"
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.services.postgres.user
|
||||
label: Database username
|
||||
default: "molgenis"
|
||||
description: "Set user of the database scheme"
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.services.postgres.password
|
||||
label: Database password
|
||||
default: "molgenis"
|
||||
description: "Set the password of the database scheme"
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.resources.limits.memory
|
||||
label: Container memory limit
|
||||
default: 1250Mi
|
||||
description: "Memory limit for this MOLGENIS container"
|
||||
type: enum
|
||||
options:
|
||||
- "1250Mi"
|
||||
- "2500Mi"
|
||||
required: true
|
||||
group: "Resources"
|
||||
- variable: molgenis.resources.requests.memory
|
||||
label: Container memory reservation
|
||||
default: 1250Mi
|
||||
description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
|
||||
type: enum
|
||||
options:
|
||||
- "1250Mi"
|
||||
- "2500Mi"
|
||||
required: true
|
||||
group: "Resources"
|
||||
- variable: molgenis.javaOpts.maxHeapSpace
|
||||
label: Maximum heap space (JVM)
|
||||
default: "1g"
|
||||
description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
|
||||
type: enum
|
||||
options:
|
||||
- "1g"
|
||||
- "2g"
|
||||
group: "Resources"
|
||||
- variable: persistence.enabled
|
||||
default: true
|
||||
description: "Do you want to use persistence"
|
||||
type: boolean
|
||||
required: true
|
||||
group: "Persistence"
|
||||
label: Persistence
|
||||
show_subquestion_if: true
|
||||
subquestions:
|
||||
- variable: persistence.retain
|
||||
default: false
|
||||
description: "Do you want to retain the persistent volume"
|
||||
type: boolean
|
||||
label: Retain volume
|
||||
- variable: molgenis.persistence.size
|
||||
default: "5Gi"
|
||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
||||
type: enum
|
||||
options:
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "20Gi"
|
||||
label: Size MOLGENIS filestore
|
||||
- variable: elasticsearch.persistence.size
|
||||
default: "5Gi"
|
||||
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
|
||||
type: enum
|
||||
options:
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "50Gi"
|
||||
label: Size for ElasticSearch data
|
||||
- variable: postgres.persistence.size
|
||||
default: "5Gi"
|
||||
description: "Size of PostgreSQL data (directory that is persist: /var/lib/postgresql/data/pgdata)"
|
||||
type: enum
|
||||
options:
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "50Gi"
|
||||
label: Size for PostgreSQL data
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
1. Get the application URL by running these commands:
|
||||
{{- if .Values.ingress.enabled }}
|
||||
{{- range .Values.ingress.hosts }}
|
||||
http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
|
||||
{{- end }}
|
||||
{{- else if contains "NodePort" .Values.service.type }}
|
||||
export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
|
||||
export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
|
||||
echo http://$NODE_IP:$NODE_PORT
|
||||
{{- else if contains "LoadBalancer" .Values.service.type }}
|
||||
NOTE: It may take a few minutes for the LoadBalancer IP to be available.
|
||||
You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
|
||||
export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
|
||||
echo http://$SERVICE_IP:{{ .Values.service.port }}
|
||||
{{- else if contains "ClusterIP" .Values.service.type }}
|
||||
export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
|
||||
echo "Visit http://127.0.0.1:8080 to use your application"
|
||||
kubectl port-forward $POD_NAME 8080:80
|
||||
{{- end }}
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
{{/* vim: set filetype=mustache: */}}
|
||||
{{/*
|
||||
Expand the name of the chart.
|
||||
*/}}
|
||||
{{- define "molgenis.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 "molgenis.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 "molgenis.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
|
@ -1,153 +0,0 @@
|
|||
apiVersion: apps/v1beta2
|
||||
kind: Deployment
|
||||
metadata:
|
||||
{{- with .Values.ingress.annotations }}
|
||||
annotations:
|
||||
{{ toYaml . | indent 4 }}
|
||||
{{- end }}
|
||||
name: {{ template "molgenis.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
strategy:
|
||||
type: Recreate
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
spec:
|
||||
containers:
|
||||
- name: molgenis
|
||||
{{- with .Values.molgenis }}
|
||||
image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: molgenis.home
|
||||
value: /home/molgenis
|
||||
- name: opencpu.uri.host
|
||||
value: {{ .services.opencpu.host }}
|
||||
- name: elasticsearch.transport.addresses
|
||||
value: {{ .services.elasticsearch.transportAddresses }}
|
||||
- name: elasticsearch.cluster.name
|
||||
value: {{ .services.elasticsearch.clusterName }}
|
||||
- name: db_uri
|
||||
value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
|
||||
- name: db_user
|
||||
value: {{ .services.postgres.user }}
|
||||
- name: db_password
|
||||
value: {{ .services.postgres.password }}
|
||||
- name: admin.password
|
||||
value: {{ .adminPassword }}
|
||||
- name: CATALINA_OPTS
|
||||
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
ports:
|
||||
- containerPort: 8080
|
||||
{{- if $.Values.persistence.enabled }}
|
||||
volumeMounts:
|
||||
- name: molgenis-nfs
|
||||
mountPath: /home/molgenis
|
||||
{{- end }}
|
||||
livenessProbe:
|
||||
httpGet:
|
||||
path: /
|
||||
port: 8080
|
||||
initialDelaySeconds: 60
|
||||
periodSeconds: 5
|
||||
failureThreshold: 25
|
||||
successThreshold: 1
|
||||
readinessProbe:
|
||||
httpGet:
|
||||
path: /api/v2/version
|
||||
port: 8080
|
||||
initialDelaySeconds: 120
|
||||
periodSeconds: 30
|
||||
failureThreshold: 3
|
||||
successThreshold: 1
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: elasticsearch
|
||||
{{- with .Values.elasticsearch }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: cluster.name
|
||||
value: {{ .clusterName }}
|
||||
- name: bootstrap.memory_lock
|
||||
value: "true"
|
||||
- name: ES_JAVA_OPTS
|
||||
value: "{{ .javaOpts }}"
|
||||
- name: xpack.security.enabled
|
||||
value: "false"
|
||||
- name: discovery.type
|
||||
value: single-node
|
||||
ports:
|
||||
- containerPort: 9200
|
||||
- containerPort: 9300
|
||||
{{- if $.Values.persistence.enabled }}
|
||||
volumeMounts:
|
||||
- name: elasticsearch-nfs
|
||||
mountPath: /usr/share/elasticsearch/data
|
||||
{{- end }}
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: postgres
|
||||
{{- with .Values.postgres }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: POSTGRES_USER
|
||||
value: {{ $.Values.molgenis.services.postgres.user }}
|
||||
- name: POSTGRES_PASSWORD
|
||||
value: {{ $.Values.molgenis.services.postgres.password }}
|
||||
- name: POSTGRES_DB
|
||||
value: {{ $.Values.molgenis.services.postgres.scheme }}
|
||||
ports:
|
||||
- containerPort: 5432
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- if $.Values.persistence.enabled }}
|
||||
volumeMounts:
|
||||
- name: postgres-nfs
|
||||
mountPath: /var/lib/postgresql/data
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
||||
|
||||
{{- if .Values.persistence.enabled }}
|
||||
volumes:
|
||||
- name: molgenis-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.molgenis.persistence.claim }}
|
||||
- name: elasticsearch-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
||||
- name: postgres-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.postgres.persistence.claim }}
|
||||
{{- end }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
{{- with .Values.affinity }}
|
||||
affinity:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
{{- with .Values.tolerations }}
|
||||
tolerations:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
|
|
@ -1,38 +0,0 @@
|
|||
{{- if .Values.ingress.enabled -}}
|
||||
{{- $fullName := include "molgenis.fullname" . -}}
|
||||
{{- $ingressPath := .Values.ingress.path -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
{{- with .Values.ingress.annotations }}
|
||||
annotations:
|
||||
{{ toYaml . | indent 4 }}
|
||||
{{- end }}
|
||||
spec:
|
||||
{{- if .Values.ingress.tls }}
|
||||
tls:
|
||||
{{- range .Values.ingress.tls }}
|
||||
- hosts:
|
||||
{{- range .hosts }}
|
||||
- {{ . }}
|
||||
{{- end }}
|
||||
secretName: {{ .secretName }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
rules:
|
||||
{{- range .Values.ingress.hosts }}
|
||||
- host: {{ .name }}
|
||||
http:
|
||||
paths:
|
||||
- path: {{ $ingressPath }}
|
||||
backend:
|
||||
serviceName: {{ $fullName }}
|
||||
servicePort: {{ $.Values.service.port }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
{{- if .Values.persistence.enabled -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.elasticsearch.persistence.claim }}
|
||||
annotations:
|
||||
{{- if .Values.persistence.retain }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
||||
{{- else }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
||||
{{- end }}
|
||||
spec:
|
||||
accessModes:
|
||||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.elasticsearch.persistence.size }}
|
||||
{{- end }}
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
{{- if .Values.persistence.enabled -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.molgenis.persistence.claim }}
|
||||
annotations:
|
||||
{{- if .Values.persistence.retain }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
||||
{{- else }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
||||
{{- end }}
|
||||
spec:
|
||||
accessModes:
|
||||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.molgenis.persistence.size }}
|
||||
{{- end }}
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
{{- if .Values.molgenis.services.postgres.embedded }}
|
||||
{{- if .Values.persistence.enabled }}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.postgres.persistence.claim }}
|
||||
annotations:
|
||||
{{- if .Values.persistence.retain }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
||||
{{- else }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
||||
{{- end }}
|
||||
spec:
|
||||
accessModes:
|
||||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.postgres.persistence.size }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
|
@ -1,29 +0,0 @@
|
|||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ template "molgenis.fullname" . }}
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
spec:
|
||||
type: {{ .Values.service.type }}
|
||||
{{- if .Values.service.firewall.enabled }}
|
||||
loadBalancerSourceRanges:
|
||||
{{- if .Values.service.firewall.kind eq "umcg" }}
|
||||
{{- range $index, $rule := .Values.service.firewall.umcg.rules }}
|
||||
- {{ $rule }}
|
||||
{{- end }}
|
||||
{{- else }}
|
||||
{{- range $index, $rule := .Values.service.firewall.cluster.rules }}
|
||||
- {{ $rule }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
ports:
|
||||
- name: molgenis
|
||||
port: {{ .Values.service.port }}
|
||||
selector:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
# Default values for molgenis.
|
||||
|
||||
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"
|
||||
path: /
|
||||
hosts:
|
||||
- name: test.molgenis.org
|
||||
tls: []
|
||||
|
||||
molgenis:
|
||||
image:
|
||||
repository: registry.hub.docker.com
|
||||
name: molgenis/molgenis-app
|
||||
tag: stable
|
||||
pullPolicy: Always
|
||||
adminPassword:
|
||||
javaOpts:
|
||||
maxHeapSpace: "1g"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 1250Mi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 1250Mi
|
||||
persistence:
|
||||
claim: molgenis-nfs-claim
|
||||
size: 5Gi
|
||||
services:
|
||||
opencpu:
|
||||
host: localhost
|
||||
elasticsearch:
|
||||
transportAddresses: localhost:9300
|
||||
clusterName: molgenis
|
||||
postgres:
|
||||
embedded: false
|
||||
host: localhost
|
||||
scheme: molgenis
|
||||
user: molgenis
|
||||
password: molgenis
|
||||
|
||||
elasticsearch:
|
||||
image:
|
||||
repository: docker.elastic.co/elasticsearch/elasticsearch
|
||||
tag: 5.5.3
|
||||
pullPolicy: IfNotPresent
|
||||
javaOpts: "-Xms1g -Xmx1g"
|
||||
clusterName: molgenis
|
||||
resources:
|
||||
limits:
|
||||
cpu: 2
|
||||
memory: 3Gi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 1Gi
|
||||
persistence:
|
||||
claim: elasticsearch-nfs-claim
|
||||
size: 5Gi
|
||||
|
||||
postgres:
|
||||
image:
|
||||
repository: postgres
|
||||
tag: 9.6-alpine
|
||||
pullPolicy: IfNotPresent
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 250Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 250Mi
|
||||
persistence:
|
||||
claim: postgres-nfs-claim
|
||||
size: 5Gi
|
||||
|
||||
persistence:
|
||||
enabled: true
|
||||
retain: false
|
||||
|
||||
nodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
Loading…
Reference in New Issue