added rstudio

This commit is contained in:
sido 2018-11-06 06:42:18 +01:00
parent 5e0ee2e5e7
commit 653d1db124
16 changed files with 300 additions and 192 deletions

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# 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

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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

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# 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

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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"

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{{/* 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 -}}

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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 }}

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{{- 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 }}

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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 }}

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# 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: {}

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

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@ -32,106 +32,4 @@ questions:
type: string type: string
required: true required: true
group: "Provisioning" 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"

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@ -42,13 +42,7 @@ spec:
- name: admin.password - name: admin.password
value: "{{ .adminPassword }}" value: "{{ .adminPassword }}"
- name: CATALINA_OPTS - 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: ports:
- containerPort: 8080 - containerPort: 8080
{{- if $.Values.persistence.enabled }} {{- if $.Values.persistence.enabled }}
@ -73,13 +67,7 @@ spec:
failureThreshold: 3 failureThreshold: 3
successThreshold: 1 successThreshold: 1
resources: 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 }} {{- end }}
{{- if .Values.persistence.enabled }} {{- if .Values.persistence.enabled }}

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@ -26,19 +26,15 @@ spec:
{{- end }} {{- end }}
{{- end }} {{- end }}
rules: 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: http:
paths: paths:
- path: {{ $ingressPath }} - path: {{ $ingressPath }}
backend: backend:
serviceName: {{ $fullName }} serviceName: {{ $fullName }}
servicePort: {{ $.Values.service.port }} servicePort: {{ $.Values.service.port }}
{{- end }}
{{- end }}
{{- end }} {{- end }}

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@ -15,11 +15,5 @@ spec:
- ReadWriteMany - ReadWriteMany
resources: resources:
requests: 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 }} {{- end }}

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@ -15,11 +15,5 @@ spec:
- ReadWriteMany - ReadWriteMany
resources: resources:
requests: 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 }} {{- end }}

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@ -4,68 +4,30 @@ replicaCount: 1
service: service:
type: LoadBalancer type: LoadBalancer
firewall:
enabled: false
kind: "umcg"
umcg:
rules:
- 127.0.0.1/32
cluster:
rules:
- 127.0.0.1/32
port: 8080 port: 8080
ingress: ingress:
enabled: true enabled: true
annotations: annotations:
nginx.ingress.kubernetes.io/proxy-body-size: "0" 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: / path: /
tls: [] tls: []
opal: opal:
advanced: false 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: image:
repository: registry.hub.docker.com repository: registry.hub.docker.com
name: obiba/opal name: obiba/opal
@ -86,6 +48,10 @@ rserver:
tag: latest tag: latest
pullPolicy: IfNotPresent pullPolicy: IfNotPresent
mysql:
persistence:
size: 10Gi
persistence: persistence:
enabled: true enabled: true
retain: false retain: false