added rstudio

charts/molgenis-rstudio/.helmignore

@@ -0,0 +1,21 @@
+# 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

charts/molgenis-rstudio/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: RStudio stack for MOLGENIS
+name: molgenis-rstudio
+version: 0.0.1
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-opencpu/catalog-molgenis-rstudio.svg
+home: https://www.rocker.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-rstudio/README.md

@@ -0,0 +1,37 @@
+# MOLGENIS - RStudio Helm Chart
+
+An RStudio instance to support DataSHIELD users in setting up a central analysis server instance.
+
+## Containers
+
+This chart will deploy the following container:
+
+- molgenis-rstudio (with DataSHIELD packages)
+
+## Provisioning
+You can choose for the RStudio image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com. 
+You need to fill out 2 properties to determine which repository you are going to use.
+
+- ```rstudio.image.repository```
+- ```rstudio.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.
+
+```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
+
+To push it to the registry

charts/molgenis-rstudio/questions.yml

@@ -0,0 +1,31 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: rstudio.environment
+  label: Environment
+  default: development
+  type: enum
+  options:
+  - development
+  - test
+  - acceptence
+  - production
+  group: "Provisioning"
+- variable: rstudio.image.repository
+  label: Registry
+  default: "registry.hub.docker.com"
+  description: "Select a registry to pull from"
+  type: enum
+  options:
+  - "registry.hub.docker.com"
+  - "registry.molgenis.org"
+  required: true
+  group: "Provisioning"
+- variable: rstudio.image.tag
+  label: Version
+  default: ""
+  description: "Select a RStudio version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"

charts/molgenis-rstudio/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "rstudio.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "rstudio.fullname" -}}
+{{- if .Values.fullnameOverride -}}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- $name := default .Chart.Name .Values.nameOverride -}}
+{{- if contains $name .Release.Name -}}
+{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "rstudio.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

charts/molgenis-rstudio/templates/deployment.yaml

@@ -0,0 +1,35 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "rstudio.fullname" . }}
+  labels:
+    app: {{ template "rstudio.name" . }}
+    chart: {{ template "rstudio.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "rstudio.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "rstudio.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+      {{- with .Values.rstudio }}
+      - name: {{ .name }}
+        image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+        imagePullPolicy: {{ .image.pullPolicy }}
+        ports:
+        - containerPort: {{ .service.port }}
+      {{- end }}
+
+

charts/molgenis-rstudio/templates/ingress.yaml

@@ -0,0 +1,44 @@
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app:  {{ $.Values.rstudio.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:
+  {{- if .Values.environment -eq "development" }}
+  - host: "analysis.dev.molgenis.org"
+  {{- else if .Values.environment -eq "test" }}
+  - host: "analysis.test.molgenis.org"
+  {{- else if .Values.environment -eq "acceptance" }}
+  - host: "analysis.accept.molgenis.org"
+  {{- else }}
+  - host: "analysis.molgenis.org"
+  {{- end }}
+    http:
+      paths:
+        - path: {{ default "/" .path }}
+          backend:
+            serviceName: {{ $.Values.rstudio.service.name }}
+            servicePort: {{ $.Values.rstudio.service.port }}
+{{- if .tls }}
+  tls:
+  - hosts:
+    - {{ .name }}
+    secretName: {{ .tlsSecret }}
+{{- end }}
+---
+{{- end }}
+{{- end }}

charts/molgenis-rstudio/templates/service.yaml

@@ -0,0 +1,20 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.rstudio.service.name }}
+  labels:
+    app: {{ .Values.rstudio.service.name }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.rstudio.service.type }}
+  loadBalancerSourceRanges:
+  {{- range $index, $rule := .Values.rstudio.service.firewall }}
+    - {{ $rule }}
+  {{- end }}
+  ports:
+    - name: {{ .Values.rstudio.service.name }}
+      port: {{ .Values.rstudio.service.port }}
+  selector:
+    app: {{ template "rstudio.name" . }}
+    release: {{ .Release.Name }}

charts/molgenis-rstudio/values.yaml

@@ -0,0 +1,40 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+rstudio:
+  environment: development
+  name: rstudio
+  strategy:
+    type: Recreate
+  restartPolicy: Always
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/rstudio
+    tag: stable
+    pullPolicy: Always
+  service:
+    name: rstudio
+    type: LoadBalancer
+    port: 8787
+
+ingress:
+  enabled: true
+  annotations: {
+    kubernetes.io/ingress.class: "nginx",
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  }
+  path: /
+  hosts:
+  - name: analysis.molgenis.org
+  tls: []
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

charts/opal/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: Opal - helm stack (in BETA)
 name: opal
-version: 0.5.4
+version: 0.0.1
 sources:
 - https://git.webhosting.rug.nl/opal/opal-ops-docker-helm.git
 icon: https://git.webhosting.rug.nl/opal/opal-ops-docker-helm/

charts/opal/questions.yml

@@ -32,106 +32,4 @@ questions:
   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: "Services"
-  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.advanced
-  label: Advanced mode
-  default: false
-  description: "Do you want to override the default values in advanced mode"
-  type: boolean
-  required: true
-  group: "Advanced"
-  show_subquestion_if: true
-  subquestions:
-  - 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.services.opencpu.host
-    label: OpenCPU cluster
-    default: "molgenis-opencpu.opencpu"
-    description: "Specify the OpenCPU cluster"
-    type: string
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.embedded
-    label: Postgres embedded
-    default: true
-    description: "Do you want an embedded postgres"
-    type: boolean
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.host
-    label: Postgres cluster location
-    default: "localhost"
-    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: persistence.retain
-    default: false
-    description: "Do you want to retain the persistent volume"
-    type: boolean
-    label: Retain volume
-    group: "Persistence"
-  - variable: persistence.molgenis.size
-    default: "default"
-    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
-    type: enum
-    options:
-    - "default"
-    - "5Gi"
-    - "10Gi"
-    - "30Gi"
-    label: Size MOLGENIS filestore
-    group: "Persistence"

charts/opal/templates/deployment.yaml

@@ -42,13 +42,7 @@ spec:
             - name: admin.password
               value: "{{ .adminPassword }}"
             - name: CATALINA_OPTS
-            {{- if eq .type.kind "small" }}
+              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-              value: "-Xmx{{ .type.small.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- else if eq .type.kind "medium"}}
-              value: "-Xmx{{ .type.medium.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- else }}
-              value: "-Xmx{{ .type.large.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- end }}
           ports:
             - containerPort: 8080
           {{- if $.Values.persistence.enabled }}
@@ -73,13 +67,7 @@ spec:
             failureThreshold: 3
             successThreshold: 1
           resources:
-          {{- if eq .type.kind "small" }}
+{{ toYaml .resources | indent 12 }}
-{{ toYaml .type.small.resources | indent 12 }}
-          {{- else if eq .type.kind "medium" }}
-{{ toYaml .type.medium.resources | indent 12 }}
-          {{- else }}
-{{ toYaml .type.large.resources | indent 12 }}
-          {{- end }}
         {{- end }}
 
 {{- if .Values.persistence.enabled }}

charts/opal/templates/ingress.yaml

@@ -26,19 +26,15 @@ spec:
   {{- end }}
 {{- end }}
   rules:
-    {{- if eq $.Values.opal.environment "development" }}
+  {{- if .Values.ingress.hosts }}
-    - host: {{ .Release.Name }}.dev.opal.org
+  {{- range $host := .Values.ingress.hosts }}
-    {{- else if eq $.Values.opal.environment "test" }}
+    - host: {{ $host }}
-    - host: {{ .Release.Name }}.test.opal.org
-    {{- else if eq $.Values.opal.environment "acceptance" }}
-    - host: {{ .Release.Name }}.accept.opal.org
-    {{- else }}
-    - host: {{ .Release.Name }}.opal.org
-    {{- end }}
       http:
         paths:
           - path: {{ $ingressPath }}
             backend:
               serviceName: {{ $fullName }}
               servicePort: {{ $.Values.service.port }}
+  {{- end }}
+  {{- end }}
 {{- end }}

charts/opal/templates/persistence/mysql-pvc.yaml

@@ -15,11 +15,5 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-    {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.mysql.persistence.size }}
-      storage: {{ .Values.mysql.type.small.persistence.size }}
-    {{- else if eq .Values.opal.type.kind "medium" }}
-      storage: {{ .Values.mysql.type.medium.persistence.size }}
-    {{- else }}
-      storage: {{ .Values.mysql.type.large.persistence.size }}
-    {{- end }}
 {{- end }}

charts/opal/templates/persistence/opal-pvc.yaml

@@ -15,11 +15,5 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-    {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.opal.persistence.size }}
-      storage: {{ .Values.opal.type.small.persistence.size }}
-    {{- else if eq .Values.opal.type.kind "medium" }}
-      storage: {{ .Values.opal.type.medium.persistence.size }}
-    {{- else }}
-      storage: {{ .Values.opal.type.large.persistence.size }}
-    {{- end }}
 {{- end }}

charts/opal/values.yaml

@@ -4,68 +4,30 @@ replicaCount: 1
 
 service:
   type: LoadBalancer
-  firewall:
-    enabled: false
-    kind: "umcg"
-    umcg:
-      rules:
-      - 127.0.0.1/32
-    cluster:
-      rules:
-      - 127.0.0.1/32
   port: 8080
 
 ingress:
   enabled: true
   annotations:
     nginx.ingress.kubernetes.io/proxy-body-size: "0"
-  # This will be used again when external domains need be attached to the instance
+  hosts:
-  # hosts:
+   - name: opal.dev.molgenis.org
-  # - name: test
   path: /
   tls: []
 
 opal:
   advanced: false
-  type:
+  javaOpts:
-    kind: medium
+    maxHeapSpace: "4g"
-    small:
+  resources:
-      javaOpts:
+    limits:
-        maxHeapSpace: "2g"
+    cpu: 4
-      resources:
+    memory: 4Gi
-        limits:
+  requests:
-          cpu: 2
+    cpu: 200m
-          memory: 2Gi
+    memory: 4Gi
-        requests:
+  persistence:
-          cpu: 200m
+    size: 10Gi
-          memory: 2Gi
-      persistence:
-        size: 5Gi
-    medium:
-      javaOpts:
-        maxHeapSpace: "3g"
-      resources:
-        limits:
-          cpu: 3
-          memory: 3Gi
-        requests:
-          cpu: 200m
-          memory: 3Gi
-      persistence:
-        size: 10Gi
-    large:
-      javaOpts:
-        maxHeapSpace: "4g"
-      resources:
-        limits:
-          cpu: 4
-          memory: 4Gi
-        requests:
-          cpu: 200m
-          memory: 4Gi
-      persistence:
-        size: 30Gi
-  environment: test
   image:
     repository: registry.hub.docker.com
     name: obiba/opal
@@ -86,6 +48,10 @@ rserver:
     tag: latest
     pullPolicy: IfNotPresent
 
+mysql:
+  persistence:
+    size: 10Gi
+
 persistence:
   enabled: true
   retain: false