Compare commits
2 Commits
chore/pipe
...
feature/s3
| Author | SHA1 | Date | |
|---|---|---|---|
| bf0e3e82a3 | |||
| 5f542e7632 |
3
.gitignore
vendored
3
.gitignore
vendored
@ -1,3 +1,2 @@
|
||||
.idea
|
||||
*.iml
|
||||
target
|
||||
*.iml
|
||||
40
Jenkinsfile
vendored
40
Jenkinsfile
vendored
@ -1,40 +0,0 @@
|
||||
pipeline {
|
||||
agent {
|
||||
kubernetes {
|
||||
label 'helm'
|
||||
}
|
||||
}
|
||||
stages {
|
||||
stage('Test') {
|
||||
steps {
|
||||
container('chart-testing') {
|
||||
sh "chart_test.sh --no-install --all"
|
||||
}
|
||||
}
|
||||
}
|
||||
stage('Package') {
|
||||
steps {
|
||||
container('chart-testing'){
|
||||
sh 'mkdir target'
|
||||
sh 'for dir in charts/*; do helm package --destination target "$dir"; done'
|
||||
}
|
||||
}
|
||||
}
|
||||
stage('Deploy') {
|
||||
when {
|
||||
branch 'master'
|
||||
}
|
||||
steps {
|
||||
container('vault') {
|
||||
script {
|
||||
env.NEXUS_USER = sh(script: 'vault read -field=username secret/ops/account/nexus', returnStdout: true)
|
||||
env.NEXUS_PWD = sh(script: 'vault read -field=password secret/ops/account/nexus', returnStdout: true)
|
||||
}
|
||||
}
|
||||
container('alpine') {
|
||||
sh 'set +x; for chart in target/*; do curl -L -u $NEXUS_USER:$NEXUS_PWD http://registry.molgenis.org/repository/helm/ --upload-file "$chart"; done'
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
21
README.md
21
README.md
@ -104,7 +104,6 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
|
||||
- [Jenkins](molgenis-jenkins/README.md)
|
||||
- [NEXUS](molgenis-nexus/README.md)
|
||||
- [HTTPD](molgenis-httpd/README.md)
|
||||
- [MOLGENIS](molgenis/README.md)
|
||||
- [MOLGENIS preview](molgenis-preview/README.md)
|
||||
- [MOLGENIS vault](molgenis-vault/README.md)
|
||||
|
||||
@ -123,26 +122,6 @@ You can you need to know to easily develop and deploy helm-charts
|
||||
|
||||
Do it in the root of the project where the Chart.yaml is located
|
||||
It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
|
||||
- ```helm package .```
|
||||
|
||||
You can create a package which can be uploaded in the molgenis helm repository
|
||||
|
||||
- ```helm publish```
|
||||
You still have to create an ```index.yaml``` for the chart. You can do this by executing this command: ```helm repo index #directory name of helm chart#```
|
||||
|
||||
Then you can upload it by executing:
|
||||
|
||||
- ```curl -v --user #username#:#password# --upload-file index.yaml https://registry.molgenis.org/repository/helm/#chart name#/index.yml```
|
||||
- ```curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz```
|
||||
|
||||
Now you have to add the repository locally to use in your ```requirements.yaml```.
|
||||
|
||||
- ```helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis```
|
||||
|
||||
- ```helm dep build```
|
||||
|
||||
You can build your dependencies (create a ```charts``` directory and install the chart in it) of the helm-chart.
|
||||
|
||||
- ```helm list```
|
||||
|
||||
Lists all installed releases
|
||||
|
||||
Binary file not shown.
@ -1,8 +0,0 @@
|
||||
# Helm in Jenkins
|
||||
|
||||
To be able to run helm inside a jenkins pod, you'll need to
|
||||
* create a role in the namespace where tiller is installed
|
||||
* bind that role to the user that jenkins pods run as
|
||||
|
||||
This directory contains yaml for these resources.
|
||||
See also https://github.com/helm/helm/blob/master/docs/rbac.md
|
||||
@ -1,13 +0,0 @@
|
||||
apiVersion: rbac.authorization.k8s.io/v1beta1
|
||||
kind: RoleBinding
|
||||
metadata:
|
||||
name: tiller-jenkins-binding
|
||||
namespace: kube-system
|
||||
roleRef:
|
||||
apiGroup: rbac.authorization.k8s.io
|
||||
kind: Role
|
||||
name: tiller-user
|
||||
subjects:
|
||||
- kind: ServiceAccount
|
||||
name: default
|
||||
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
|
||||
@ -1,69 +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.
|
||||
|
||||
```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
|
||||
|
||||
To push it to the registry
|
||||
|
||||
|
||||
|
||||
@ -1,55 +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 }}
|
||||
@ -1,15 +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 }}
|
||||
@ -1,13 +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: {}
|
||||
@ -1,12 +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
|
||||
home: https://www.opencpu.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
@ -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"
|
||||
@ -1,35 +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: {}
|
||||
@ -1,13 +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 }}
|
||||
@ -1,10 +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 }}
|
||||
@ -1,21 +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 }}
|
||||
@ -5,8 +5,4 @@ name: molgenis-httpd
|
||||
version: 0.1.0
|
||||
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-httpd/catalogIcon-molgenis-httpd.svg
|
||||
home: http://httpd.apache.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg
|
||||
|
Before Width: | Height: | Size: 89 KiB After Width: | Height: | Size: 89 KiB |
@ -48,4 +48,4 @@ nodeSelector: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
affinity: {}
|
||||
@ -1,11 +1,8 @@
|
||||
name: molgenis-jenkins
|
||||
home: https://jenkins.io/
|
||||
version: 0.8.1
|
||||
appVersion: 2.138.1
|
||||
version: 0.7.0
|
||||
appVersion: 2.121
|
||||
description: Molgenis installation for the jenkins chart.
|
||||
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-jenkins/catalogIcon-molgenis-jenkins.svg
|
||||
maintainers:
|
||||
- name: fdlk
|
||||
- name: sidohaakma
|
||||
@ -75,10 +75,6 @@ Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.w
|
||||
| `secret.gogs.user` | username for the account | `p281392` |
|
||||
| `secret.gogs.token` | token for the account | `xxxx` |
|
||||
|
||||
|
||||
#### Slack
|
||||
The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
|
||||
|
||||
#### Legacy:
|
||||
|
||||
##### Docker Hub
|
||||
|
Before Width: | Height: | Size: 133 KiB After Width: | Height: | Size: 133 KiB |
BIN
molgenis-jenkins/charts/jenkins-0.16.4.tgz
Normal file
BIN
molgenis-jenkins/charts/jenkins-0.16.4.tgz
Normal file
Binary file not shown.
@ -1,6 +1,6 @@
|
||||
dependencies:
|
||||
- name: jenkins
|
||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||
version: 0.18.0
|
||||
version: 0.16.4
|
||||
digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
|
||||
generated: 2018-09-27T11:00:15.795416984+02:00
|
||||
generated: 2018-06-27T14:36:23.172954738+02:00
|
||||
@ -3,18 +3,17 @@ jenkins:
|
||||
HostName: jenkins.molgenis.org
|
||||
ServiceType: ClusterIP
|
||||
InstallPlugins:
|
||||
- kubernetes:1.12.6
|
||||
- kubernetes:1.12.0
|
||||
- workflow-aggregator:2.5
|
||||
- workflow-job:2.25
|
||||
- workflow-job:2.21
|
||||
- credentials-binding:1.16
|
||||
- git:3.9.1
|
||||
- github-branch-source:2.3.6
|
||||
- kubernetes-credentials-provider:0.10
|
||||
- blueocean:1.8.3
|
||||
- kubernetes-credentials-provider:0.9
|
||||
- blueocean:1.6.2
|
||||
- github-oauth:0.29
|
||||
- gogs-webhook:1.0.14
|
||||
- github-scm-trait-commit-skip:0.1.1
|
||||
- slack:2.3
|
||||
- sauce-ondemand:1.176
|
||||
Security:
|
||||
UseGitHub: false
|
||||
GitHub:
|
||||
@ -83,18 +82,6 @@ jenkins:
|
||||
<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>
|
||||
@ -144,17 +131,6 @@ jenkins:
|
||||
<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">
|
||||
@ -208,17 +184,6 @@ jenkins:
|
||||
<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">
|
||||
@ -272,17 +237,6 @@ jenkins:
|
||||
<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">
|
||||
@ -336,17 +290,6 @@ jenkins:
|
||||
<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">
|
||||
@ -400,17 +343,6 @@ jenkins:
|
||||
<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">
|
||||
@ -484,12 +416,6 @@ jenkins:
|
||||
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
|
||||
@ -521,104 +447,7 @@ jenkins:
|
||||
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: {}
|
||||
helm:
|
||||
Label: helm
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
Containers:
|
||||
chart-testing:
|
||||
Image: "quay.io/helmpack/chart-testing"
|
||||
ImageTag: v1.1.0
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
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
|
||||
NodeSelector: {}
|
||||
|
||||
# secret contains configuration for the kubernetes secrets that jenkins can access
|
||||
#secret contains configuration for the kubernetes secrets that jenkins can access
|
||||
secret:
|
||||
# vault configures the vault secret
|
||||
vault:
|
||||
@ -640,4 +469,4 @@ secret:
|
||||
# dockerHubPassword contains password for hub.docker.com
|
||||
dockerHub:
|
||||
user: molgenisci
|
||||
password: xxxx
|
||||
password: xxxx
|
||||
@ -2,11 +2,7 @@ apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: Nexus stack for MOLGENIS
|
||||
name: molgenis-nexus
|
||||
version: 0.4.2
|
||||
version: 0.3.0
|
||||
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
|
||||
home: https://www.sonatype.com/nexus-repository-oss
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg
|
||||
28
molgenis-nexus/README.md
Normal file
28
molgenis-nexus/README.md
Normal file
@ -0,0 +1,28 @@
|
||||
# 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 container
|
||||
- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
|
||||
|
||||
## 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.
|
||||
|
||||
|
||||
|
Before Width: | Height: | Size: 42 KiB After Width: | Height: | Size: 42 KiB |
34
molgenis-nexus/templates/deployments/httpd-deployment.yaml
Normal file
34
molgenis-nexus/templates/deployments/httpd-deployment.yaml
Normal file
@ -0,0 +1,34 @@
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Deployment
|
||||
metadata:
|
||||
creationTimestamp: null
|
||||
name: {{ .Values.httpd.name }}
|
||||
labels:
|
||||
app: {{ .Values.httpd.name }}
|
||||
environment: {{ .Values.environment }}
|
||||
spec:
|
||||
replicas: {{ .Values.replicaCount }}
|
||||
strategy:
|
||||
type: {{ .Values.httpd.strategy.type }}
|
||||
selector:
|
||||
matchLabels:
|
||||
app: {{ .Values.httpd.selector }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ .Values.httpd.name }}
|
||||
creationTimestamp: null
|
||||
spec:
|
||||
restartPolicy: {{ .Values.httpd.restartPolicy }}
|
||||
containers:
|
||||
- name: {{ .Values.httpd.name }}
|
||||
image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}"
|
||||
imagePullPolicy: {{ .Values.httpd.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.httpd.hostname }}
|
||||
ports:
|
||||
- containerPort: {{ .Values.httpd.port }}
|
||||
resources: {}
|
||||
@ -19,14 +19,18 @@ spec:
|
||||
app: {{ .Values.nexus.name }}
|
||||
creationTimestamp: null
|
||||
spec:
|
||||
volumes:
|
||||
- name: {{ .Values.persistence.name }}
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.persistence.name }}
|
||||
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
||||
initContainers:
|
||||
- name: nexus-nfs
|
||||
- name: volume-mount-nexus
|
||||
image: busybox
|
||||
command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
|
||||
command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
|
||||
volumeMounts:
|
||||
- name: molgenis-nexus-nfs
|
||||
mountPath: "/nexus-data"
|
||||
- name: {{ .Values.persistence.name }}
|
||||
mountPath: "{{ .Values.persistence.mountPath }}"
|
||||
containers:
|
||||
- name: {{ .Values.nexus.name }}
|
||||
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
||||
@ -35,31 +39,6 @@ spec:
|
||||
- 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
|
||||
- name: {{ .Values.persistence.name }}
|
||||
mountPath: "/nexus-data"
|
||||
|
||||
volumes:
|
||||
- name: molgenis-nexus-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.persistence.claim }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
@ -5,7 +5,7 @@ kind: Ingress
|
||||
metadata:
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
labels:
|
||||
app: {{ $.Values.nexusProxy.name }}
|
||||
app: httpd
|
||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
||||
release: "{{ $.Release.Name }}"
|
||||
heritage: "{{ $.Release.Service }}"
|
||||
@ -25,8 +25,8 @@ spec:
|
||||
paths:
|
||||
- path: {{ default "/" .path }}
|
||||
backend:
|
||||
serviceName: {{ $.Values.nexusProxy.name }}
|
||||
servicePort: {{ $.Values.nexusProxy.port }}
|
||||
serviceName: httpd
|
||||
servicePort: 80
|
||||
{{- if .tls }}
|
||||
tls:
|
||||
- hosts:
|
||||
13
molgenis-nexus/templates/services/httpd-service.yaml
Normal file
13
molgenis-nexus/templates/services/httpd-service.yaml
Normal file
@ -0,0 +1,13 @@
|
||||
apiVersion: v1
|
||||
kind: Service
|
||||
metadata:
|
||||
name: {{ .Values.httpd.name }}
|
||||
labels:
|
||||
app: {{ .Values.httpd.name }}
|
||||
spec:
|
||||
type: {{ .Values.httpd.service.type }}
|
||||
ports:
|
||||
- name: {{ .Values.httpd.name }}
|
||||
port: {{ .Values.httpd.port }}
|
||||
selector:
|
||||
app: {{ .Values.httpd.selector }}
|
||||
16
molgenis-nexus/templates/volumes/nexus-pv.yaml
Normal file
16
molgenis-nexus/templates/volumes/nexus-pv.yaml
Normal file
@ -0,0 +1,16 @@
|
||||
apiVersion: v1
|
||||
kind: PersistentVolume
|
||||
metadata:
|
||||
name: {{ .Values.persistence.name }}
|
||||
labels:
|
||||
name: nfs2
|
||||
spec:
|
||||
storageClassName: {{ .Values.persistence.storageClass }}
|
||||
capacity:
|
||||
storage: {{ .Values.persistence.size }}
|
||||
accessModes:
|
||||
- {{ .Values.persistence.accessMode }}
|
||||
persistentVolumeReclaimPolicy: {{ .Values.persistence.reclaimPolicy }}
|
||||
nfs:
|
||||
server: {{ .Values.persistence.server }}
|
||||
path: {{ .Values.persistence.mountPath }}
|
||||
11
molgenis-nexus/templates/volumes/nexus-pvc.yaml
Normal file
11
molgenis-nexus/templates/volumes/nexus-pvc.yaml
Normal file
@ -0,0 +1,11 @@
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.persistence.name }}
|
||||
spec:
|
||||
storageClassName: {{ .Values.persistence.storageClass }}
|
||||
accessModes:
|
||||
- {{ .Values.persistence.accessMode }}
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.persistence.size }}
|
||||
82
molgenis-nexus/values.yaml
Normal file
82
molgenis-nexus/values.yaml
Normal file
@ -0,0 +1,82 @@
|
||||
# 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: sonatype/nexus3
|
||||
tag: latest
|
||||
pullPolicy: Always
|
||||
port:
|
||||
docker: 5000
|
||||
ui: 8081
|
||||
path:
|
||||
dockerV2: v2
|
||||
service:
|
||||
type: ClusterIP
|
||||
|
||||
httpd:
|
||||
name: httpd
|
||||
hostname: registry.molgenis.org
|
||||
strategy:
|
||||
type: Recreate
|
||||
selector: httpd
|
||||
restartPolicy: Always
|
||||
image:
|
||||
repository: registry.webhosting.rug.nl/molgenis/httpd
|
||||
tag: lts
|
||||
pullPolicy: Always
|
||||
port: 80
|
||||
service:
|
||||
type: LoadBalancer
|
||||
|
||||
|
||||
ingress:
|
||||
enabled: true
|
||||
annotations: {}
|
||||
# kubernetes.io/ingress.class: nginx
|
||||
# kubernetes.io/tls-acme: "true"
|
||||
path: /
|
||||
hosts:
|
||||
- name: registry.molgenis.org
|
||||
tls: []
|
||||
# - secretName: chart-example-tls
|
||||
# hosts:
|
||||
# - chart-example.local
|
||||
|
||||
persistence:
|
||||
name: molgenis-nexus-data
|
||||
storageClass: nfs-class
|
||||
size: 30G
|
||||
reclaimPolicy: Retain
|
||||
server: 192.168.64.12
|
||||
accessMode: ReadWriteMany
|
||||
mountPath: /gcc/molgenis/nexus
|
||||
|
||||
|
||||
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: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
8
molgenis-preview/Chart.yaml
Normal file
8
molgenis-preview/Chart.yaml
Normal file
@ -0,0 +1,8 @@
|
||||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS - helm stack for testing purposes
|
||||
name: molgenis-preview
|
||||
version: 0.2.0
|
||||
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-preview/catalogIcon-molgenis.svg
|
||||
16
molgenis-preview/README.md
Normal file
16
molgenis-preview/README.md
Normal file
@ -0,0 +1,16 @@
|
||||
# MOLGENIS preview
|
||||
This chart is used for testing purposes. It can be used by data managers or developers to test MOLGENIS (e.g. integration testing).
|
||||
|
||||
## Containers
|
||||
This chart spins up a complete stack to run MOLGENIS. The created containers are:
|
||||
|
||||
- MOLGENIS
|
||||
- PostgreSQL
|
||||
- Elasticsearch
|
||||
- OpenCPU
|
||||
|
||||
## Rancher
|
||||
You can spin up a test instance by navigating to https://rancher.molgenis.org:7777 and login with your LDAP-account.
|
||||
|
||||
Go to the test-environment and click on "Launch". Search for MOLGENIS.
|
||||
|
||||
|
Before Width: | Height: | Size: 77 KiB After Width: | Height: | Size: 77 KiB |
61
molgenis-preview/questions.yml
Normal file
61
molgenis-preview/questions.yml
Normal file
@ -0,0 +1,61 @@
|
||||
|
||||
categories:
|
||||
- MOLGENIS
|
||||
questions:
|
||||
- variable: ingress.hosts[0].name
|
||||
default: "test.molgenis.org"
|
||||
description: "Hostname for your stack"
|
||||
type: hostname
|
||||
required: true
|
||||
group: "Services and Load Balancing"
|
||||
label: Hostname
|
||||
- variable: molgenis.image.repository
|
||||
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: "MOLGENIS - Version"
|
||||
label: Registry
|
||||
- variable: molgenis.image.tag
|
||||
default: "stable"
|
||||
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
|
||||
type: string
|
||||
required: true
|
||||
group: "MOLGENIS - Version"
|
||||
label: Version
|
||||
- variable: molgenis.resources.limits.cpu
|
||||
default: 1
|
||||
description: "CPU limit for this MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "1"
|
||||
- "2"
|
||||
- "3"
|
||||
- "4"
|
||||
required: true
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: CPU limit
|
||||
- variable: molgenis.resources.limits.memory
|
||||
default: 1250Mi
|
||||
description: "Memory limit for this MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "1250Mi"
|
||||
- "1500Mi"
|
||||
- "2000Mi"
|
||||
- "2500Mi"
|
||||
required: true
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: Memory limit
|
||||
- variable: molgenis.javaOpts
|
||||
default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
description: "Java runtime options for the MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
- "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: Java memory options
|
||||
124
molgenis-preview/templates/deployment.yaml
Normal file
124
molgenis-preview/templates/deployment.yaml
Normal file
@ -0,0 +1,124 @@
|
||||
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 }}
|
||||
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: localhost
|
||||
- name: elasticsearch.transport.addresses
|
||||
value: localhost:9300
|
||||
- name: elasticsearch.cluster.name
|
||||
value: {{ $.Values.elasticsearch.clusterName }}
|
||||
- name: db_uri
|
||||
value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
|
||||
- name: db_user
|
||||
value: {{ $.Values.postgres.user }}
|
||||
- name: db_password
|
||||
value: {{ $.Values.postgres.password }}
|
||||
- name: admin.password
|
||||
value: {{ .adminPassword }}
|
||||
- name: CATALINA_OPTS
|
||||
value: "{{ .javaOpts }}"
|
||||
ports:
|
||||
- containerPort: 8080
|
||||
# livenessProbe:
|
||||
# httpGet:
|
||||
# path: /
|
||||
# port: 8080
|
||||
# readinessProbe:
|
||||
# httpGet:
|
||||
# path: /api/v2/version
|
||||
# port: 8080
|
||||
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
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: postgres
|
||||
{{- with .Values.postgres }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: POSTGRES_USER
|
||||
value: {{ .user }}
|
||||
- name: POSTGRES_PASSWORD
|
||||
value: {{ .password }}
|
||||
- name: POSTGRES_DB
|
||||
value: {{ .db }}
|
||||
ports:
|
||||
- containerPort: 5432
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: opencpu
|
||||
{{- with .Values.opencpu }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
ports:
|
||||
- containerPort: 8004
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- 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 }}
|
||||
@ -4,7 +4,7 @@
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
name: {{ $fullName }}
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
@ -33,6 +33,6 @@ spec:
|
||||
- path: {{ $ingressPath }}
|
||||
backend:
|
||||
serviceName: {{ $fullName }}
|
||||
servicePort: {{ $.Values.service.port }}
|
||||
servicePort: 8080
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
@ -9,18 +9,6 @@ metadata:
|
||||
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 }}
|
||||
82
molgenis-preview/values.yaml
Normal file
82
molgenis-preview/values.yaml
Normal file
@ -0,0 +1,82 @@
|
||||
# Default values for molgenis.
|
||||
|
||||
replicaCount: 1
|
||||
|
||||
service:
|
||||
type: LoadBalancer
|
||||
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.molgenis.org
|
||||
name: molgenis/molgenis-app
|
||||
tag: 7.0.0-SNAPSHOT
|
||||
pullPolicy: Always
|
||||
adminPassword: admin
|
||||
javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 1250Mi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 1Gi
|
||||
|
||||
postgres:
|
||||
image:
|
||||
repository: postgres
|
||||
tag: 9.6-alpine
|
||||
pullPolicy: IfNotPresent
|
||||
user: molgenis
|
||||
password: molgenis
|
||||
db: molgenis
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 250Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 250Mi
|
||||
|
||||
elasticsearch:
|
||||
image:
|
||||
repository: docker.elastic.co/elasticsearch/elasticsearch
|
||||
tag: 5.5.3
|
||||
pullPolicy: IfNotPresent
|
||||
javaOpts: "-Xms512m -Xmx512m"
|
||||
clusterName: molgenis
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 1500Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 1Gi
|
||||
|
||||
opencpu:
|
||||
image:
|
||||
repository: molgenis/opencpu
|
||||
tag: latest
|
||||
pullPolicy: Always
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 512Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 256Mi
|
||||
|
||||
nodeSelector: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
@ -2,9 +2,5 @@ apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS vault
|
||||
name: molgenis-vault
|
||||
version: 0.1.1
|
||||
version: 0.2.1
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg
|
||||
home: https://github.com/coreos/vault-operator
|
||||
maintainers:
|
||||
- name: fdlk
|
||||
- name: sidohaakma
|
||||
@ -13,21 +13,25 @@ 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).
|
||||
Define credentials for an S3 compatible backup bucket.
|
||||
See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/walkthrough/backup-operator.md).
|
||||
> Default values backup to the minio play server.
|
||||
You can host the stable/minio chart to backup to a bucket on the cluster.
|
||||
|
||||
| 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` |
|
||||
| Parameter | Description | Default |
|
||||
| -------------------- | ---------------------------------------- | ------------------------------------------ |
|
||||
| `s3.accessKeyId` | key id storage account | `Q3AM3UQ867SPQQA43P2F` |
|
||||
| `s3.secretAccessKey` | secret access key of storage account | `zuf+tfteSlswRu7BJ86wekitnifILbZam1KYY3TG` |
|
||||
| `s3.region` | region of the storage server | `us-east-1` |
|
||||
| `s3.endpoint` | endpoint for the storage server | `https://play.minio.io:9000` |
|
||||
| `s3.bucket` | name of the bucket on the storage server | `vault` |
|
||||
|
||||
### Backup job
|
||||
Define the schedule of the backup job
|
||||
|
||||
| Parameter | Description | Default |
|
||||
| -------------------- | ---------------------------- | ------------- |
|
||||
| `backupJob.enable` | Enable backup cronjob | `true` |
|
||||
| `backupJob.suspend` | Suspend backup cronjob | `false` |
|
||||
| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1` |
|
||||
|
||||
### UI
|
||||
|
Before Width: | Height: | Size: 46 KiB After Width: | Height: | Size: 46 KiB |
13
molgenis-vault/resources/backup.yaml
Normal file
13
molgenis-vault/resources/backup.yaml
Normal file
@ -0,0 +1,13 @@
|
||||
apiVersion: "etcd.database.coreos.com/v1beta2"
|
||||
kind: "EtcdBackup"
|
||||
metadata:
|
||||
name: vault-backup
|
||||
namespace: "vault-operator"
|
||||
spec:
|
||||
etcdEndpoints: ["https://vault-etcd-client:2379"]
|
||||
storageType: S3
|
||||
clientTLSSecret: vault-etcd-client-tls
|
||||
s3:
|
||||
path: vault/backup-manual
|
||||
awsSecret: aws
|
||||
endpoint: http://minio.minio.svc:9000
|
||||
@ -9,7 +9,8 @@ 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
|
||||
backupStorageType: S3
|
||||
s3:
|
||||
path: vault/backup-<name>
|
||||
awsSecret: aws
|
||||
endpoint: http://minio.minio.svc:9000
|
||||
17
molgenis-vault/templates/NOTES.txt
Normal file
17
molgenis-vault/templates/NOTES.txt
Normal file
@ -0,0 +1,17 @@
|
||||
Vault operator created
|
||||
|
||||
Next steps:
|
||||
|
||||
* Manually create a vault using resources/vault.yaml
|
||||
* Manually restore a backup using resources/restore.yaml
|
||||
* Unseal the vault pods
|
||||
|
||||
{{ if .Values.backupJob.suspend }}
|
||||
!!!!!! BACKUP JOB SUSPENDED !!!!!!
|
||||
{{ else }}
|
||||
{{- if .Values.s3.endpoint -}}
|
||||
Backing up to non-standard s3 endpoint {{ .Values.s3.endpoint }} {{ else -}}
|
||||
Backing up to S3 on aws {{ end -}}
|
||||
in bucket {{ .Values.s3.bucket }}.
|
||||
!! Make sure to check if the backups succeed !!
|
||||
{{ end }}
|
||||
10
molgenis-vault/templates/aws-secret.yaml
Normal file
10
molgenis-vault/templates/aws-secret.yaml
Normal file
@ -0,0 +1,10 @@
|
||||
# Secret to access s3 compatible store
|
||||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
name: aws
|
||||
type: Opaque
|
||||
data:
|
||||
config: {{ printf "[default]\nregion = %s" .Values.s3.region | b64enc | quote }}
|
||||
credentials: {{ printf "[default]\naws_access_key_id = %s\naws_secret_access_key = %s\n" .Values.s3.accessKeyId .Values.s3.secretAccessKey | b64enc | quote }}
|
||||
|
||||
@ -11,8 +11,14 @@ data:
|
||||
generateName: vault-backup-
|
||||
spec:
|
||||
etcdEndpoints: ["https://vault-etcd-client:2379"]
|
||||
storageType: ABS
|
||||
storageType: S3
|
||||
clientTLSSecret: vault-etcd-client-tls
|
||||
abs:
|
||||
path: vault/backup.<NOW>
|
||||
absSecret: abs
|
||||
s3:
|
||||
path: {{ .Values.s3.bucket }}/backup.<NOW>
|
||||
awsSecret: aws
|
||||
{{- if .Values.s3.endpoint }}
|
||||
endpoint: {{ .Values.s3.endpoint }}
|
||||
{{- end }}
|
||||
{{- if hasKey .Values.s3 "forcePathStyle" }}
|
||||
forcePathStyle: {{ .Values.s3.forcePathStyle }}
|
||||
{{- end }}
|
||||
@ -1,10 +1,10 @@
|
||||
{{- if .Values.backupJob.enable }}
|
||||
# cronjob that creates etcdbackups using the etcd backup serviceaccount
|
||||
apiVersion: batch/v1beta1
|
||||
kind: CronJob
|
||||
metadata:
|
||||
name: etcd-backup
|
||||
spec:
|
||||
suspend: {{ .Values.backupJob.suspend }}
|
||||
schedule: {{ .Values.backupJob.schedule | quote }}
|
||||
jobTemplate:
|
||||
spec:
|
||||
@ -26,5 +26,4 @@ spec:
|
||||
volumes:
|
||||
- name: backup-config
|
||||
configMap:
|
||||
name: backup-config
|
||||
{{- end }}
|
||||
name: backup-config
|
||||
@ -2,19 +2,26 @@
|
||||
# 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
|
||||
# s3 configures s3 backup storage
|
||||
s3:
|
||||
# accessKey for the s3 storage account
|
||||
accessKeyId: Q3AM3UQ867SPQQA43P2F
|
||||
# secretAccessKey for the s3 storage account
|
||||
secretAccessKey: zuf+tfteSlswRu7BJ86wekitnifILbZam1KYY3TG
|
||||
# region
|
||||
region: us-east-1
|
||||
# endpoint for the s3 storage
|
||||
endpoint: https://play.minio.io:9000
|
||||
# forcePathStyle if set to true forces requests to use path style
|
||||
# (host/bucket instead of bucket.host)
|
||||
forcePathStyle: true
|
||||
# bucket is the name of the bucket
|
||||
bucket: vault
|
||||
|
||||
# backupjob describes the backup cronjob
|
||||
backupJob:
|
||||
# enable enables the backup job
|
||||
enable: true
|
||||
# suspend suspends the backup job
|
||||
suspend: false
|
||||
# schedule gives the cron schedule for the backup job
|
||||
schedule: "0 12 * * 1"
|
||||
|
||||
@ -40,10 +47,12 @@ etcd-operator:
|
||||
tag: v0.9.2
|
||||
backupOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
repository: fdlk/etcd-operator
|
||||
tag: latest
|
||||
restoreOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
repository: fdlk/etcd-operator
|
||||
tag: latest
|
||||
|
||||
ui:
|
||||
name: "vault-ui"
|
||||
@ -70,10 +79,10 @@ ui:
|
||||
# limits:
|
||||
# cpu: 100m
|
||||
# memory: 128Mi
|
||||
# requests:
|
||||
#requests:
|
||||
# cpu: 100m
|
||||
# memory: 128Mi
|
||||
nodeSelector: {}
|
||||
vault:
|
||||
auth: GITHUB
|
||||
url: https://vault.vault-operator:8200
|
||||
url: https://vault.vault-operator:8200
|
||||
@ -1,12 +1,8 @@
|
||||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS - helm stack (in BETA)
|
||||
name: molgenis
|
||||
version: 0.4.3
|
||||
name: molgenis-beta
|
||||
version: 0.3.0
|
||||
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
|
||||
home: http://molgenis.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||
@ -5,8 +5,6 @@ This chart is used for acceptance and production use cases.
|
||||
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:
|
||||
@ -23,19 +21,6 @@ The three properties you need to specify are:
|
||||
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)
|
||||
@ -97,16 +82,15 @@ 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'
|
||||
- ```persistence.enabled```
|
||||
|
||||
You can also choose to retain the volume of the NFS.
|
||||
- ```persistence.retain``` default 'false'
|
||||
- ```persistence.retain```
|
||||
|
||||
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```
|
||||
@ -116,9 +100,6 @@ 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:
|
||||
@ -135,4 +116,7 @@ You can now view the persistent volume claims and the attached volumes.
|
||||
| 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```.
|
||||
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```.
|
||||
|
||||
## Firewall
|
||||
Is defined at cluster level. This chart does not facilitate firewall configuration.
|
||||
1024
molgenis/catalogIcon-molgenis.svg
Normal file
1024
molgenis/catalogIcon-molgenis.svg
Normal file
File diff suppressed because it is too large
Load Diff
|
After Width: | Height: | Size: 77 KiB |
@ -8,7 +8,7 @@ questions:
|
||||
description: "Hostname for your stack"
|
||||
type: hostname
|
||||
required: true
|
||||
group: "Load balancing"
|
||||
group: "Load Balancing"
|
||||
- variable: molgenis.image.repository
|
||||
label: Registry
|
||||
default: "registry.hub.docker.com"
|
||||
@ -33,24 +33,6 @@ questions:
|
||||
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"
|
||||
@ -58,43 +40,34 @@ questions:
|
||||
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
|
||||
- variable: molgenis.services.postgres.host
|
||||
label: Postgres cluster location
|
||||
default: "postgresql.molgenis-postgresql.svc"
|
||||
description: "Set the location of the postgres cluster"
|
||||
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"
|
||||
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
|
||||
@ -125,7 +98,7 @@ questions:
|
||||
- "2g"
|
||||
group: "Resources"
|
||||
- variable: persistence.enabled
|
||||
default: true
|
||||
default: false
|
||||
description: "Do you want to use persistence"
|
||||
type: boolean
|
||||
required: true
|
||||
@ -139,29 +112,20 @@ questions:
|
||||
type: boolean
|
||||
label: Retain volume
|
||||
- variable: molgenis.persistence.size
|
||||
default: "5Gi"
|
||||
default: "30Gi"
|
||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
||||
type: enum
|
||||
options:
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "20Gi"
|
||||
- "30Gi"
|
||||
- "50Gi"
|
||||
- "100Gi"
|
||||
label: Size MOLGENIS filestore
|
||||
- variable: elasticsearch.persistence.size
|
||||
default: "5Gi"
|
||||
default: "50Gi"
|
||||
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
|
||||
- "100Gi"
|
||||
- "200Gi"
|
||||
label: Size for ElasticSearch data
|
||||
19
molgenis/templates/NOTES.txt
Normal file
19
molgenis/templates/NOTES.txt
Normal file
@ -0,0 +1,19 @@
|
||||
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 }}
|
||||
@ -2,7 +2,7 @@
|
||||
{{/*
|
||||
Expand the name of the chart.
|
||||
*/}}
|
||||
{{- define "opencpu.name" -}}
|
||||
{{- define "molgenis.name" -}}
|
||||
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
|
||||
@ -11,7 +11,7 @@ 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" -}}
|
||||
{{- define "molgenis.fullname" -}}
|
||||
{{- if .Values.fullnameOverride -}}
|
||||
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
||||
{{- else -}}
|
||||
@ -27,6 +27,6 @@ If release name contains chart name it will be used as a full name.
|
||||
{{/*
|
||||
Create chart name and version as used by the chart label.
|
||||
*/}}
|
||||
{{- define "opencpu.chart" -}}
|
||||
{{- define "molgenis.chart" -}}
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||
{{- end -}}
|
||||
@ -17,8 +17,6 @@ spec:
|
||||
matchLabels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
strategy:
|
||||
type: Recreate
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
@ -99,33 +97,11 @@ spec:
|
||||
- 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
|
||||
@ -134,9 +110,6 @@ spec:
|
||||
- name: elasticsearch-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
||||
- name: postgres-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.postgres.persistence.claim }}
|
||||
{{- end }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
38
molgenis/templates/ingress.yaml
Normal file
38
molgenis/templates/ingress.yaml
Normal file
@ -0,0 +1,38 @@
|
||||
{{- if .Values.ingress.enabled -}}
|
||||
{{- $fullName := include "molgenis.fullname" . -}}
|
||||
{{- $ingressPath := .Values.ingress.path -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: {{ $fullName }}
|
||||
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: 8080
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user