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7 Commits
chore/pipe
...
deploy-tes
| Author | SHA1 | Date | |
|---|---|---|---|
| f8de505ed6 | |||
| af00229be0 | |||
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| 2d84fb08a8 | |||
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| acbd380a0c | |||
| e54f958add |
1
.gitignore
vendored
1
.gitignore
vendored
@ -1,3 +1,2 @@
|
|||||||
.idea
|
.idea
|
||||||
*.iml
|
*.iml
|
||||||
target
|
|
||||||
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'
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
24
README.md
24
README.md
@ -104,9 +104,7 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
|
|||||||
- [Jenkins](molgenis-jenkins/README.md)
|
- [Jenkins](molgenis-jenkins/README.md)
|
||||||
- [NEXUS](molgenis-nexus/README.md)
|
- [NEXUS](molgenis-nexus/README.md)
|
||||||
- [HTTPD](molgenis-httpd/README.md)
|
- [HTTPD](molgenis-httpd/README.md)
|
||||||
- [MOLGENIS](molgenis/README.md)
|
- [MOLNIGES preview](molgenis-preview/README.md)
|
||||||
- [MOLGENIS preview](molgenis-preview/README.md)
|
|
||||||
- [MOLGENIS vault](molgenis-vault/README.md)
|
|
||||||
|
|
||||||
### Useful commands
|
### Useful commands
|
||||||
You can you need to know to easily develop and deploy helm-charts
|
You can you need to know to easily develop and deploy helm-charts
|
||||||
@ -123,26 +121,6 @@ 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
|
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
|
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```
|
- ```helm list```
|
||||||
|
|
||||||
Lists all installed releases
|
Lists all installed releases
|
||||||
|
|||||||
@ -1,115 +0,0 @@
|
|||||||
# Molgenis Jenkins Helm Chart
|
|
||||||
|
|
||||||
Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin.
|
|
||||||
Wraps [the kuberenetes jenkins chart](https://github.com/kubernetes/charts/tree/master/stable/jenkins), see documentation there!
|
|
||||||
|
|
||||||
## Chart Details
|
|
||||||
|
|
||||||
This chart will do the following:
|
|
||||||
|
|
||||||
* 1 x Jenkins Master with port 8080 exposed on an external ClusterIP
|
|
||||||
* All using Kubernetes Deployments
|
|
||||||
|
|
||||||
## Installing the Chart
|
|
||||||
|
|
||||||
Usually, you'll be deploying this to the molgenis cluster.
|
|
||||||
In the [Rancher Catalog](https://rancher.molgenis.org:7443/g/catalog), add the latest version of this repository.
|
|
||||||
In the [molgenis cluster management page](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/apps), choose the
|
|
||||||
catalog, pick the molgenis-jenkins app from the catalog and deploy it.
|
|
||||||
|
|
||||||
## Configuration
|
|
||||||
|
|
||||||
When deploying, you can paste values into the Rancher Answers to override the defaults in this chart.
|
|
||||||
Array values can be added as {value, value, value}.
|
|
||||||
```
|
|
||||||
jenkins.Master.HostName=jenkins.molgenis.org
|
|
||||||
jenkins.Master.AdminPassword=pa$$word
|
|
||||||
jenkins.Persistence.Enabled=false
|
|
||||||
jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29}
|
|
||||||
jenkins.Master.Security.UseGitHub=false
|
|
||||||
## if UseGitHub=true
|
|
||||||
jenkins.Master.Security.GitHub.ClientID=id
|
|
||||||
jenkins.Master.Security.GitHub.ClientSecret=S3cr3t
|
|
||||||
## end UseGitHub=true
|
|
||||||
PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
|
|
||||||
```
|
|
||||||
|
|
||||||
You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
|
|
||||||
> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
|
|
||||||
|
|
||||||
### GitHub Authentication delegation
|
|
||||||
You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
|
|
||||||
|
|
||||||
### Secrets
|
|
||||||
|
|
||||||
When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
|
|
||||||
|
|
||||||
You can override the values at deploy time but otherwise also configure them
|
|
||||||
[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
|
|
||||||
|
|
||||||
#### Vault
|
|
||||||
|
|
||||||
The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
|
|
||||||
| `secret.vault.token` | Token to log into the hashicorp vault | `xxxx` |
|
|
||||||
| `secret.vault.addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
|
|
||||||
| `secret.vault.skipVerify` | Skip verification of the https connection | `1` |
|
|
||||||
|
|
||||||
#### GitHub
|
|
||||||
|
|
||||||
Token used by Jenkins to authenticate on GitHub.
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| --------------------- | ------------------------ | ------------------ |
|
|
||||||
| `secret.gitHub.user` | username for the account | `molgenis-jenkins` |
|
|
||||||
| `secret.gitHub.token` | token for the account | `xxxx` |
|
|
||||||
|
|
||||||
#### Gogs
|
|
||||||
|
|
||||||
Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| ------------------- | ------------------------ | --------- |
|
|
||||||
| `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
|
|
||||||
|
|
||||||
Account used in pipeline builds to push docker images to `hub.docker.com`.
|
|
||||||
> They should read `secret/gcc/account/dockerhub` from vault instead!
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| --------------------------- | ------------------------ | --------------- |
|
|
||||||
| `secret.dockerHub.user` | username for the account | `molgenisci` |
|
|
||||||
| `secret.dockerHub.password` | password for the account | `xxxx` |
|
|
||||||
|
|
||||||
##### Registry
|
|
||||||
|
|
||||||
Account used in pipeline builds to push docker images to `registry.molgenis.org`.
|
|
||||||
> They should read `secret/ops/account/nexus` from vault instead!
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| --------------------------- | ------------------------ | --------- |
|
|
||||||
| `secret.dockerHub.user` | username for the account | `admin` |
|
|
||||||
| `secret.dockerHub.password` | password for the account | `xxxx` |
|
|
||||||
|
|
||||||
## Command line use
|
|
||||||
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
|
||||||
|
|
||||||
Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart.
|
|
||||||
For example,
|
|
||||||
|
|
||||||
```bash
|
|
||||||
$ helm install --name jenkins -f values.yaml molgenis-jenkins
|
|
||||||
```
|
|
||||||
|
|
||||||
> **Tip**: You can use the default [values.yaml](values.yaml)
|
|
||||||
|
|
||||||
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
|
|
||||||
@ -1,17 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Secret
|
|
||||||
metadata:
|
|
||||||
name: molgenis-jenkins-registry-secret
|
|
||||||
labels:
|
|
||||||
app: {{ template "jenkins.fullname" . }}
|
|
||||||
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
|
||||||
release: "{{ .Release.Name }}"
|
|
||||||
heritage: "{{ .Release.Service }}"
|
|
||||||
annotations: {
|
|
||||||
# description - can not be a label as spaces are not allowed
|
|
||||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
|
|
||||||
}
|
|
||||||
type: Opaque
|
|
||||||
data:
|
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
|
||||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
|
||||||
@ -1,69 +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"
|
|
||||||
@ -1,32 +0,0 @@
|
|||||||
{{/* vim: set filetype=mustache: */}}
|
|
||||||
{{/*
|
|
||||||
Expand the name of the chart.
|
|
||||||
*/}}
|
|
||||||
{{- define "opencpu.name" -}}
|
|
||||||
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/*
|
|
||||||
Create a default fully qualified app name.
|
|
||||||
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
|
||||||
If release name contains chart name it will be used as a full name.
|
|
||||||
*/}}
|
|
||||||
{{- define "opencpu.fullname" -}}
|
|
||||||
{{- if .Values.fullnameOverride -}}
|
|
||||||
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- else -}}
|
|
||||||
{{- $name := default .Chart.Name .Values.nameOverride -}}
|
|
||||||
{{- if contains $name .Release.Name -}}
|
|
||||||
{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- else -}}
|
|
||||||
{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
{{- end -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/*
|
|
||||||
Create chart name and version as used by the chart label.
|
|
||||||
*/}}
|
|
||||||
{{- define "opencpu.chart" -}}
|
|
||||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
@ -1,35 +0,0 @@
|
|||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Deployment
|
|
||||||
metadata:
|
|
||||||
{{- with .Values.ingress.annotations }}
|
|
||||||
annotations:
|
|
||||||
{{ toYaml . | indent 4 }}
|
|
||||||
{{- end }}
|
|
||||||
name: {{ template "opencpu.fullname" . }}
|
|
||||||
labels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
chart: {{ template "opencpu.chart" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
spec:
|
|
||||||
replicas: {{ .Values.replicaCount }}
|
|
||||||
selector:
|
|
||||||
matchLabels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
template:
|
|
||||||
metadata:
|
|
||||||
labels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
spec:
|
|
||||||
containers:
|
|
||||||
{{- with .Values.opencpu }}
|
|
||||||
- name: {{ .name }}
|
|
||||||
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
|
||||||
imagePullPolicy: {{ .image.pullPolicy }}
|
|
||||||
ports:
|
|
||||||
- containerPort: {{ .service.port }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,36 +0,0 @@
|
|||||||
{{- if .Values.ingress.enabled }}
|
|
||||||
{{- range .Values.ingress.hosts }}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Ingress
|
|
||||||
metadata:
|
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
|
||||||
labels:
|
|
||||||
app: {{ $.Values.opencpu.name }}
|
|
||||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
|
||||||
release: "{{ $.Release.Name }}"
|
|
||||||
heritage: "{{ $.Release.Service }}"
|
|
||||||
annotations:
|
|
||||||
{{- if .tls }}
|
|
||||||
ingress.kubernetes.io/secure-backends: "true"
|
|
||||||
{{- end }}
|
|
||||||
{{- range $key, $value := .annotations }}
|
|
||||||
{{ $key }}: {{ $value | quote }}
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
rules:
|
|
||||||
- host: {{ .name }}
|
|
||||||
http:
|
|
||||||
paths:
|
|
||||||
- path: {{ default "/" .path }}
|
|
||||||
backend:
|
|
||||||
serviceName: {{ $.Values.opencpu.service.name }}
|
|
||||||
servicePort: {{ $.Values.opencpu.service.port }}
|
|
||||||
{{- if .tls }}
|
|
||||||
tls:
|
|
||||||
- hosts:
|
|
||||||
- {{ .name }}
|
|
||||||
secretName: {{ .tlsSecret }}
|
|
||||||
{{- end }}
|
|
||||||
---
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
@ -1,20 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Service
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.opencpu.service.name }}
|
|
||||||
labels:
|
|
||||||
app: {{ .Values.opencpu.service.name }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
spec:
|
|
||||||
type: {{ .Values.opencpu.service.type }}
|
|
||||||
loadBalancerSourceRanges:
|
|
||||||
{{- range $index, $rule := .Values.opencpu.service.firewall }}
|
|
||||||
- {{ $rule }}
|
|
||||||
{{- end }}
|
|
||||||
ports:
|
|
||||||
- name: {{ .Values.opencpu.service.name }}
|
|
||||||
port: {{ .Values.opencpu.service.port }}
|
|
||||||
selector:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
@ -1,41 +0,0 @@
|
|||||||
# Default values for nexus.
|
|
||||||
# This is a YAML-formatted file.
|
|
||||||
# Declare variables to be passed into your templates.
|
|
||||||
|
|
||||||
replicaCount: 1
|
|
||||||
|
|
||||||
environment: production
|
|
||||||
|
|
||||||
opencpu:
|
|
||||||
name: opencpu
|
|
||||||
strategy:
|
|
||||||
type: Recreate
|
|
||||||
restartPolicy: Always
|
|
||||||
image:
|
|
||||||
repository: registry.hub.docker.com
|
|
||||||
name: molgenis/opencpu
|
|
||||||
tag: stable
|
|
||||||
pullPolicy: Always
|
|
||||||
service:
|
|
||||||
name: opencpu
|
|
||||||
type: LoadBalancer
|
|
||||||
port: 8004
|
|
||||||
firewall:
|
|
||||||
- 145.100.224.1/24
|
|
||||||
|
|
||||||
ingress:
|
|
||||||
enabled: false
|
|
||||||
annotations: {
|
|
||||||
kubernetes.io/ingress.class: "nginx",
|
|
||||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
|
||||||
}
|
|
||||||
path: /
|
|
||||||
hosts:
|
|
||||||
- name: opencpu.molgenis.org
|
|
||||||
tls: []
|
|
||||||
|
|
||||||
nodeSelector: {}
|
|
||||||
|
|
||||||
tolerations: []
|
|
||||||
|
|
||||||
affinity: {}
|
|
||||||
@ -1,21 +0,0 @@
|
|||||||
# Patterns to ignore when building packages.
|
|
||||||
# This supports shell glob matching, relative path matching, and
|
|
||||||
# negation (prefixed with !). Only one pattern per line.
|
|
||||||
.DS_Store
|
|
||||||
# Common VCS dirs
|
|
||||||
.git/
|
|
||||||
.gitignore
|
|
||||||
.bzr/
|
|
||||||
.bzrignore
|
|
||||||
.hg/
|
|
||||||
.hgignore
|
|
||||||
.svn/
|
|
||||||
# Common backup files
|
|
||||||
*.swp
|
|
||||||
*.bak
|
|
||||||
*.tmp
|
|
||||||
*~
|
|
||||||
# Various IDEs
|
|
||||||
.project
|
|
||||||
.idea/
|
|
||||||
*.tmproj
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
appVersion: "1.0"
|
|
||||||
description: MOLGENIS vault
|
|
||||||
name: molgenis-vault
|
|
||||||
version: 0.1.1
|
|
||||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg
|
|
||||||
home: https://github.com/coreos/vault-operator
|
|
||||||
maintainers:
|
|
||||||
- name: fdlk
|
|
||||||
- name: sidohaakma
|
|
||||||
@ -1,52 +0,0 @@
|
|||||||
# MOLGENIS Vault helm chart
|
|
||||||
|
|
||||||
This chart creates a vault operator, but NO vault.
|
|
||||||
The vault operator defines a new custom resource named `vault` that you can use to create vaults.
|
|
||||||
|
|
||||||
After launching the operator, create the molgenis vault manually:
|
|
||||||
`kubectl create -f resources/vault.yaml`
|
|
||||||
|
|
||||||
That creates a new vault with two vault pods.
|
|
||||||
|
|
||||||
See https://github.com/coreos/vault-operator/blob/master/doc/user/vault.md
|
|
||||||
|
|
||||||
## Parameters
|
|
||||||
|
|
||||||
### Azure cloud credentials
|
|
||||||
Define credentials for backup to the Azure Blob Store.
|
|
||||||
See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/abs_backup.md).
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| --------------- | ----------------------------- | ------------------ |
|
|
||||||
| `abs.account` | name of storage account | `fdlkops` |
|
|
||||||
| `abs.accessKey` | access key of storage account | `xxxx` |
|
|
||||||
| `abs.cloud` | name of cloud environment | `AzurePublicCloud` |
|
|
||||||
|
|
||||||
### Backup job
|
|
||||||
Define the schedule of the backup job
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
|
||||||
| -------------------- | ---------------------------- | ------------- |
|
|
||||||
| `backupJob.enable` | Enable backup cronjob | `true` |
|
|
||||||
| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1` |
|
|
||||||
|
|
||||||
### UI
|
|
||||||
|
|
||||||
Parameter | Description | Default
|
|
||||||
--------- | ----------- | -------
|
|
||||||
`ui.replicaCount` | desired number of Vault UI pod | `1`
|
|
||||||
`ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui`
|
|
||||||
`ui.image.tag` | Vault UI container image tag | `latest`
|
|
||||||
`ui.resources` | Vault UI pod resource requests & limits | `{}`
|
|
||||||
`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}`
|
|
||||||
`ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true`
|
|
||||||
`ui.ingress.annotations` | Vault UI Ingress annotations | `{}`
|
|
||||||
`ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org`
|
|
||||||
`ui.ingress.tls` | Vault UI Ingress TLS configuration (YAML) | `[]`
|
|
||||||
`ui.vault.url` | Vault UI default vault url | `https://vault.vault-operator:8200`
|
|
||||||
`ui.vault.auth` | Vault UI login method | `GITHUB`
|
|
||||||
`ui.service.name` | Vault UI service name | `vault-ui`
|
|
||||||
`ui.service.type` | type of ui service to create | `ClusterIP`
|
|
||||||
`ui.service.externalPort` | Vault UI service target port | `8000`
|
|
||||||
`ui.service.internalPort` | Vault UI container port | `8000`
|
|
||||||
`ui.service.nodePort` | Port to be used as the service NodePort (ignored if `server.service.type` is not `NodePort`) | `0`
|
|
||||||
@ -1,627 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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|
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xmlns:svg="http://www.w3.org/2000/svg"
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||||||
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|
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xmlns:xlink="http://www.w3.org/1999/xlink"
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height="264px"
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|
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viewBox="0 0 500 264"
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|
||||||
enable-background="new 0 0 500 264"
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|
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xml:space="preserve"
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|
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sodipodi:docname="catalogIcon-molgenis-vault.svg"
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|
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inkscape:version="0.92.2 5c3e80d, 2017-08-06"><metadata
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ix7sCG3lXtmOYzsF67vf6Mce4ur2wkdMJuK/34hiZ/BAEmgCDzH/euK9smKYwHqg82Iq1DOadioa
|
|
||||||
zLpuF4RSOWAnmMqLVWrRftYP7YDYh/34h//sTN5Of0i2XPEYhAExnIivvfoftcSTUVQMGRrKYCrK
|
|
||||||
+9lCCUQI+3z0ecKRYF4JvhMwjsTFD/RgR2hr90oveqajz+Pi2P10f+AjJluueBQQMIhwg2OYACfi
|
|
||||||
PyukoUT45cRDOBVDZZGBMczZy3ywz4/1Mx57ikrWKWq3EwLGL/cjhrGH+b4e/diLzOt/4YpHAQ6g
|
|
||||||
2A0KYRxiPtjHx/oZjz1FJevE/MBOtwtiODLAofE+3zH2MN/Xox97kXn9b5n4vIrSuGpFIBFfLT5K
|
|
||||||
syYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqz
|
|
||||||
JhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMm
|
|
||||||
EV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrPmL/hk6fsEzapeAAAAAElF
|
|
||||||
TkSuQmCC
|
|
||||||
"
|
|
||||||
style="image-rendering:optimizeQuality"
|
|
||||||
preserveAspectRatio="none"
|
|
||||||
height="94.666664"
|
|
||||||
width="84" /><g
|
|
||||||
inkscape:groupmode="layer"
|
|
||||||
id="layer1"
|
|
||||||
inkscape:label="base"
|
|
||||||
style="opacity:1" /></svg>
|
|
||||||
|
Before Width: | Height: | Size: 46 KiB |
Binary file not shown.
Binary file not shown.
@ -1,9 +0,0 @@
|
|||||||
dependencies:
|
|
||||||
- name: vault-operator
|
|
||||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
|
||||||
version: 0.1.1
|
|
||||||
- name: etcd-operator
|
|
||||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
|
||||||
version: 0.8.0
|
|
||||||
digest: sha256:47aa645df7dfce9760905800321599de05995ae50090735d45310936dbaa46de
|
|
||||||
generated: 2018-09-06T18:59:39.861922543+02:00
|
|
||||||
@ -1,7 +0,0 @@
|
|||||||
dependencies:
|
|
||||||
- name: vault-operator
|
|
||||||
version: ^0.1.1
|
|
||||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
|
||||||
- name: etcd-operator
|
|
||||||
version: ^0.8.0
|
|
||||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
|
||||||
@ -1,15 +0,0 @@
|
|||||||
# Use kubectl create -f restore.yaml to manually execute a restore of the vault
|
|
||||||
apiVersion: "etcd.database.coreos.com/v1beta2"
|
|
||||||
kind: "EtcdRestore"
|
|
||||||
metadata:
|
|
||||||
# The restore CR name must be the same as spec.etcdCluster.name
|
|
||||||
name: vault-etcd
|
|
||||||
namespace: vault-operator
|
|
||||||
spec:
|
|
||||||
etcdCluster:
|
|
||||||
# The namespace is the same as this EtcdRestore CR
|
|
||||||
name: vault-etcd
|
|
||||||
backupStorageType: ABS
|
|
||||||
abs:
|
|
||||||
path: vault/backup-<specify the backup name>
|
|
||||||
absSecret: abs
|
|
||||||
@ -1,9 +0,0 @@
|
|||||||
# Use kubectl create -f vault.yaml to manually create a vault
|
|
||||||
apiVersion: "vault.security.coreos.com/v1alpha1"
|
|
||||||
kind: "VaultService"
|
|
||||||
metadata:
|
|
||||||
name: "vault"
|
|
||||||
namespace: "vault-operator"
|
|
||||||
spec:
|
|
||||||
nodes: 2
|
|
||||||
version: "0.9.1-0"
|
|
||||||
@ -1,13 +0,0 @@
|
|||||||
Vault operator created
|
|
||||||
|
|
||||||
Next steps:
|
|
||||||
|
|
||||||
* Manually create a vault using resources/vault.yaml
|
|
||||||
* Manually restore a backup using resources/backup.yaml
|
|
||||||
* Unseal the vault pods
|
|
||||||
|
|
||||||
{{ if .Values.backupJob.enable }}
|
|
||||||
!! Make sure to check if the backups succeed !!
|
|
||||||
{{ else }}
|
|
||||||
!!!!!! NO BACKUPS CONFIGURED !!!!!!
|
|
||||||
{{ end }}
|
|
||||||
@ -1,54 +0,0 @@
|
|||||||
{{/*
|
|
||||||
Define vault ui fullname
|
|
||||||
*/}}
|
|
||||||
{{- define "vault.ui.fullname" -}}
|
|
||||||
{{- printf "%s-ui" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/*
|
|
||||||
Define vault service url for the ui
|
|
||||||
*/}}
|
|
||||||
{{- define "vault.service.url" -}}
|
|
||||||
{{- printf "https://%s:8200" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/* See https://github.com/helm/helm/issues/4535 */}}
|
|
||||||
{{- define "call-nested" }}
|
|
||||||
{{- $dot := index . 0 }}
|
|
||||||
{{- $subchart := index . 1 }}
|
|
||||||
{{- $template := index . 2 }}
|
|
||||||
{{- include $template (dict "Chart" (dict "Name" $subchart) "Values" (index $dot.Values $subchart) "Release" $dot.Release "Capabilities" $dot.Capabilities) }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
{{/* vim: set filetype=mustache: */}}
|
|
||||||
{{/*
|
|
||||||
Expand the name of the chart.
|
|
||||||
*/}}
|
|
||||||
{{- define "molgenis-vault.name" -}}
|
|
||||||
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/*
|
|
||||||
Create a default fully qualified app name.
|
|
||||||
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
|
||||||
If release name contains chart name it will be used as a full name.
|
|
||||||
*/}}
|
|
||||||
{{- define "molgenis-vault.fullname" -}}
|
|
||||||
{{- if .Values.fullnameOverride -}}
|
|
||||||
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- else -}}
|
|
||||||
{{- $name := default .Chart.Name .Values.nameOverride -}}
|
|
||||||
{{- if contains $name .Release.Name -}}
|
|
||||||
{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- else -}}
|
|
||||||
{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
{{- end -}}
|
|
||||||
{{- end -}}
|
|
||||||
|
|
||||||
{{/*
|
|
||||||
Create chart name and version as used by the chart label.
|
|
||||||
*/}}
|
|
||||||
{{- define "molgenis-vault.chart" -}}
|
|
||||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
|
||||||
{{- end -}}
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
# Secret to access microsoft azure blob store
|
|
||||||
apiVersion: v1
|
|
||||||
kind: Secret
|
|
||||||
metadata:
|
|
||||||
name: abs
|
|
||||||
type: Opaque
|
|
||||||
stringData:
|
|
||||||
storage-account: {{ .Values.abs.account }}
|
|
||||||
storage-key: {{ .Values.abs.accessKey }}
|
|
||||||
cloud: {{ .Values.abs.cloud }}
|
|
||||||
@ -1,18 +0,0 @@
|
|||||||
# configmap to use as a template by the backup cronjob to create etcdbackup instances
|
|
||||||
apiVersion: v1
|
|
||||||
kind: ConfigMap
|
|
||||||
metadata:
|
|
||||||
name: backup-config
|
|
||||||
data:
|
|
||||||
backup_cr.yaml: |
|
|
||||||
apiVersion: "etcd.database.coreos.com/v1beta2"
|
|
||||||
kind: "EtcdBackup"
|
|
||||||
metadata:
|
|
||||||
generateName: vault-backup-
|
|
||||||
spec:
|
|
||||||
etcdEndpoints: ["https://vault-etcd-client:2379"]
|
|
||||||
storageType: ABS
|
|
||||||
clientTLSSecret: vault-etcd-client-tls
|
|
||||||
abs:
|
|
||||||
path: vault/backup.<NOW>
|
|
||||||
absSecret: abs
|
|
||||||
@ -1,30 +0,0 @@
|
|||||||
{{- if .Values.backupJob.enable }}
|
|
||||||
# cronjob that creates etcdbackups using the etcd backup serviceaccount
|
|
||||||
apiVersion: batch/v1beta1
|
|
||||||
kind: CronJob
|
|
||||||
metadata:
|
|
||||||
name: etcd-backup
|
|
||||||
spec:
|
|
||||||
schedule: {{ .Values.backupJob.schedule | quote }}
|
|
||||||
jobTemplate:
|
|
||||||
spec:
|
|
||||||
template:
|
|
||||||
spec:
|
|
||||||
serviceAccountName: {{ include "call-nested" (list . "etcd-operator" "etcd-operator.serviceAccountName") }}
|
|
||||||
containers:
|
|
||||||
- name: etcd-backup
|
|
||||||
image: lachlanevenson/k8s-kubectl
|
|
||||||
command:
|
|
||||||
- /bin/sh
|
|
||||||
- "-ec"
|
|
||||||
- |
|
|
||||||
sed -e "s|<NOW>|$(date '+%Y-%m-%d_%H:%M:%S')|g" /var/etcd_backup/backup_cr.yaml | kubectl create -f -
|
|
||||||
volumeMounts:
|
|
||||||
- name: backup-config
|
|
||||||
mountPath: /var/etcd_backup
|
|
||||||
restartPolicy: OnFailure
|
|
||||||
volumes:
|
|
||||||
- name: backup-config
|
|
||||||
configMap:
|
|
||||||
name: backup-config
|
|
||||||
{{- end }}
|
|
||||||
@ -1,30 +0,0 @@
|
|||||||
{{- if .Values.ui.ingress.enabled -}}
|
|
||||||
{{- $serviceName := include "vault.ui.fullname" . -}}
|
|
||||||
{{- $servicePort := .Values.ui.service.externalPort -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Ingress
|
|
||||||
metadata:
|
|
||||||
name: {{ template "vault.ui.fullname" . }}
|
|
||||||
labels:
|
|
||||||
app: {{ template "molgenis-vault.name" . }}
|
|
||||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
annotations:
|
|
||||||
{{- range $key, $value := .Values.ui.ingress.annotations }}
|
|
||||||
{{ $key }}: {{ $value | quote }}
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
rules:
|
|
||||||
- host: {{ .Values.ui.ingress.host }}
|
|
||||||
http:
|
|
||||||
paths:
|
|
||||||
- path:
|
|
||||||
backend:
|
|
||||||
serviceName: {{ $serviceName }}
|
|
||||||
servicePort: {{ $servicePort }}
|
|
||||||
{{- if .Values.ui.ingress.tls }}
|
|
||||||
tls:
|
|
||||||
{{ toYaml .Values.ui.ingress.tls | indent 4 }}
|
|
||||||
{{- end -}}
|
|
||||||
{{- end -}}
|
|
||||||
@ -1,23 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Service
|
|
||||||
metadata:
|
|
||||||
name: {{ template "vault.ui.fullname" . }}
|
|
||||||
labels:
|
|
||||||
app: {{ template "vault-operator.name" . }}
|
|
||||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
spec:
|
|
||||||
type: {{ .Values.ui.service.type }}
|
|
||||||
ports:
|
|
||||||
- port: {{ .Values.ui.service.externalPort }}
|
|
||||||
targetPort: {{ .Values.ui.service.internalPort }}
|
|
||||||
protocol: TCP
|
|
||||||
name: {{ .Values.ui.service.name }}
|
|
||||||
{{- if .Values.ui.service.nodePort }}
|
|
||||||
nodePort: {{ .Values.ui.service.nodePort }}
|
|
||||||
{{- end }}
|
|
||||||
selector:
|
|
||||||
app: {{ template "vault-operator.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
component: {{ .Values.ui.name }}
|
|
||||||
@ -1,50 +0,0 @@
|
|||||||
apiVersion: apps/v1beta1
|
|
||||||
kind: Deployment
|
|
||||||
metadata:
|
|
||||||
name: {{ template "vault.ui.fullname" . }}
|
|
||||||
labels:
|
|
||||||
app: {{ template "vault-operator.name" . }}
|
|
||||||
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
component: {{ .Values.ui.name }}
|
|
||||||
spec:
|
|
||||||
replicas: {{ .Values.ui.replicaCount }}
|
|
||||||
template:
|
|
||||||
metadata:
|
|
||||||
labels:
|
|
||||||
app: {{ template "vault-operator.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
component: {{ .Values.ui.name }}
|
|
||||||
spec:
|
|
||||||
containers:
|
|
||||||
- name: {{ .Values.ui.name }}
|
|
||||||
image: "{{ .Values.ui.image.repository }}:{{ .Values.ui.image.tag }}"
|
|
||||||
imagePullPolicy: {{ .Values.imagePullPolicy }}
|
|
||||||
env:
|
|
||||||
- name: VAULT_URL_DEFAULT
|
|
||||||
{{- if .Values.ui.vault.url }}
|
|
||||||
value: {{ .Values.ui.vault.url }}
|
|
||||||
{{ else }}
|
|
||||||
value: {{ template "vault.service.url" . }}
|
|
||||||
{{- end }}
|
|
||||||
- name: VAULT_AUTH_DEFAULT
|
|
||||||
value: {{ .Values.ui.vault.auth }}
|
|
||||||
- name: NODE_TLS_REJECT_UNAUTHORIZED
|
|
||||||
value: '0'
|
|
||||||
ports:
|
|
||||||
- containerPort: {{ .Values.ui.service.internalPort }}
|
|
||||||
livenessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.ui.service.internalPort }}
|
|
||||||
readinessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.ui.service.internalPort }}
|
|
||||||
resources:
|
|
||||||
{{ toYaml .Values.ui.resources | indent 12 }}
|
|
||||||
{{- if .Values.ui.nodeSelector }}
|
|
||||||
nodeSelector:
|
|
||||||
{{ toYaml .Values.ui.nodeSelector | indent 8 }}
|
|
||||||
{{- end }}
|
|
||||||
@ -1,79 +0,0 @@
|
|||||||
# Default values for molgenis-vault.
|
|
||||||
# This is a YAML-formatted file.
|
|
||||||
# Declare variables to be passed into your templates.
|
|
||||||
|
|
||||||
# abs gives details of the credentials to reach the azure backup storage
|
|
||||||
abs:
|
|
||||||
# account is the name of the Storage account
|
|
||||||
account: fdlkops
|
|
||||||
# access key for the Storage account
|
|
||||||
accessKey: xxxx
|
|
||||||
# default cloud
|
|
||||||
cloud: AzurePublicCloud
|
|
||||||
|
|
||||||
# backupjob describes the backup cronjob
|
|
||||||
backupJob:
|
|
||||||
# enable enables the backup job
|
|
||||||
enable: true
|
|
||||||
# schedule gives the cron schedule for the backup job
|
|
||||||
schedule: "0 12 * * 1"
|
|
||||||
|
|
||||||
###
|
|
||||||
# All of the config variables related to setting up the etcd-operator
|
|
||||||
# If you want more information about the variables exposed, please visit:
|
|
||||||
# https://github.com/kubernetes/charts/tree/master/stable/etcd-operator#configuration
|
|
||||||
###
|
|
||||||
etcd-operator:
|
|
||||||
deployments:
|
|
||||||
etcdOperator: true
|
|
||||||
backupOperator: true
|
|
||||||
restoreOperator: true
|
|
||||||
serviceAccount:
|
|
||||||
etcdOperatorServiceAccount:
|
|
||||||
create: true
|
|
||||||
backupOperatorServiceAccount:
|
|
||||||
create: true
|
|
||||||
restoreOperatorServiceAccount:
|
|
||||||
create: true
|
|
||||||
etcdOperator:
|
|
||||||
image:
|
|
||||||
tag: v0.9.2
|
|
||||||
backupOperator:
|
|
||||||
image:
|
|
||||||
tag: v0.9.2
|
|
||||||
restoreOperator:
|
|
||||||
image:
|
|
||||||
tag: v0.9.2
|
|
||||||
|
|
||||||
ui:
|
|
||||||
name: "vault-ui"
|
|
||||||
replicaCount: 1
|
|
||||||
image:
|
|
||||||
repository: djenriquez/vault-ui
|
|
||||||
tag: latest
|
|
||||||
service:
|
|
||||||
name: vault-ui
|
|
||||||
type: ClusterIP
|
|
||||||
externalPort: 8000
|
|
||||||
internalPort: 8000
|
|
||||||
# nodePort: 32001
|
|
||||||
ingress:
|
|
||||||
enabled: true
|
|
||||||
# Used to create Ingress record (should used with service.type: ClusterIP).
|
|
||||||
host: vault.molgenis.org
|
|
||||||
|
|
||||||
resources: {}
|
|
||||||
# We usually recommend not to specify default resources and to leave this as a conscious
|
|
||||||
# choice for the user. This also increases chances charts run on environments with little
|
|
||||||
# resources, such as Minikube. If you do want to specify resources, uncomment the following
|
|
||||||
# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
|
|
||||||
# limits:
|
|
||||||
# cpu: 100m
|
|
||||||
# memory: 128Mi
|
|
||||||
# requests:
|
|
||||||
# cpu: 100m
|
|
||||||
# memory: 128Mi
|
|
||||||
nodeSelector: {}
|
|
||||||
vault:
|
|
||||||
auth: GITHUB
|
|
||||||
url: https://vault.vault-operator:8200
|
|
||||||
@ -1,138 +0,0 @@
|
|||||||
# MOLGENIS
|
|
||||||
This chart is used for acceptance and production use cases.
|
|
||||||
|
|
||||||
## Containers
|
|
||||||
This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
|
|
||||||
|
|
||||||
- MOLGENIS
|
|
||||||
- ElasticSearch
|
|
||||||
- PostgreSQL **(optional)**
|
|
||||||
|
|
||||||
## Provisioning
|
|
||||||
You can choose from which registry you want to pull. There are 2 registries:
|
|
||||||
- https://registry.molgenis.org
|
|
||||||
- https://hub.docker.com
|
|
||||||
|
|
||||||
The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
|
|
||||||
|
|
||||||
The three properties you need to specify are:
|
|
||||||
- ```molgenis.image.repository```
|
|
||||||
- ```molgenis.image.name```
|
|
||||||
- ```molgenis.image.tag```
|
|
||||||
|
|
||||||
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
|
||||||
- ```molgenis.adminPassword```
|
|
||||||
|
|
||||||
### Firewall
|
|
||||||
Is defined at service level you can specify this attribute in the values:
|
|
||||||
|
|
||||||
- ```molgenis.firewall.enabled``` default 'false'
|
|
||||||
|
|
||||||
If set to 'true' the following options are available. One of the options below has to be set.
|
|
||||||
|
|
||||||
- ```molgenis.firewall.umcg.enabled``` default 'false'
|
|
||||||
- ```molgenis.firewall.cluster.enabled``` default 'false'
|
|
||||||
|
|
||||||
UMCG = only available within the UMCG.
|
|
||||||
Cluster = only available within the GCC cluster environment.
|
|
||||||
|
|
||||||
## Services
|
|
||||||
When you start MOLGENIS you need:
|
|
||||||
- an elasticsearch instance (5.5.6)
|
|
||||||
- an postgres instance (9.6)
|
|
||||||
|
|
||||||
You can attach additional services like:
|
|
||||||
- an opencpu instance
|
|
||||||
|
|
||||||
### Elasticsearch
|
|
||||||
You can configure elasticsearch by giving in the cluster location.
|
|
||||||
|
|
||||||
To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch.
|
|
||||||
From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
|
|
||||||
- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
|
|
||||||
|
|
||||||
To configure the index on a Elasticsearch cluster you can specify the clusterName property.
|
|
||||||
- ```molgenis.services.elasticsearch.clusterName: molgenis```
|
|
||||||
|
|
||||||
### Postgres
|
|
||||||
You can specify the location of the postgres instance by specify the following property:
|
|
||||||
- ```molgenis.services.postgres.host: localhost```
|
|
||||||
|
|
||||||
You can specify the schema by filling out this property:
|
|
||||||
- ```molgenis.services.postgres.scheme: molgenis```
|
|
||||||
|
|
||||||
You can specify credentials for the database scheme by specifying the following properties:
|
|
||||||
- ```molgenis.services.postgres.user: molgenis```
|
|
||||||
- ```molgenis.services.postgres.password: molgenis```
|
|
||||||
|
|
||||||
To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# answers for postgresql chart
|
|
||||||
postgresUser=molgenis
|
|
||||||
postgresPassword=molgenis
|
|
||||||
postgresDatabase=molgenis
|
|
||||||
persistence.enabled=false
|
|
||||||
```
|
|
||||||
|
|
||||||
### OpenCPU
|
|
||||||
You can specify the location of the OpenCPU cluster by specifying this property:
|
|
||||||
- ```molgenis.services.opencpu.host: localhost```
|
|
||||||
|
|
||||||
You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
|
|
||||||
|
|
||||||
## Resources
|
|
||||||
You can specify resources by resource type. There are 2 resource types.
|
|
||||||
- memory of container
|
|
||||||
- maximum heap space JVM
|
|
||||||
|
|
||||||
Specify memory usage of container:
|
|
||||||
- ```molgenis.resources.limits.memory```
|
|
||||||
|
|
||||||
Specify memory usage for Java JVM:
|
|
||||||
- ```molgenis.javaOpts.maxHeapSpace```
|
|
||||||
|
|
||||||
Select the resources you need dependant on the customer you need to serve.
|
|
||||||
|
|
||||||
## Persistence
|
|
||||||
You can enable persistence on your MOLGENIS stack by specifying the following property.
|
|
||||||
|
|
||||||
- ```persistence.enabled``` default 'true'
|
|
||||||
|
|
||||||
You can also choose to retain the volume of the NFS.
|
|
||||||
- ```persistence.retain``` default 'false'
|
|
||||||
|
|
||||||
The size and claim name can be specified per service. There are now two services that can be persist.
|
|
||||||
|
|
||||||
- MOLGENIS
|
|
||||||
- ElasticSearch
|
|
||||||
- PostgreSQL **(optional)**
|
|
||||||
|
|
||||||
MOLGENIS persistent properties.
|
|
||||||
- ```molgenis.persistence.claim```
|
|
||||||
- ```molgenis.persistence.size```
|
|
||||||
|
|
||||||
ElasticSearch persistent properties.
|
|
||||||
- ```elasticsearch.persistence.claim```
|
|
||||||
- ```elasticsearch.persistence.size```
|
|
||||||
|
|
||||||
PostgreSQL persistent properties.
|
|
||||||
- ```postgres.persistence.claim```
|
|
||||||
- ```postgres.persistence.size```
|
|
||||||
|
|
||||||
### Resolve you persistent volume
|
|
||||||
You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
|
|
||||||
|
|
||||||
```
|
|
||||||
kubectl get pv
|
|
||||||
```
|
|
||||||
|
|
||||||
You can now view the persistent volume claims and the attached volumes.
|
|
||||||
|
|
||||||
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
|
|
||||||
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
|
|
||||||
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
|
|
||||||
| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
|
|
||||||
|
|
||||||
You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
@ -1,167 +0,0 @@
|
|||||||
|
|
||||||
categories:
|
|
||||||
- MOLGENIS
|
|
||||||
questions:
|
|
||||||
- variable: ingress.hosts[0].name
|
|
||||||
label: Hostname
|
|
||||||
default: "test.molgenis.org"
|
|
||||||
description: "Hostname for your stack"
|
|
||||||
type: hostname
|
|
||||||
required: true
|
|
||||||
group: "Load balancing"
|
|
||||||
- variable: molgenis.image.repository
|
|
||||||
label: Registry
|
|
||||||
default: "registry.hub.docker.com"
|
|
||||||
description: "Select a registry to pull from"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "registry.hub.docker.com"
|
|
||||||
- "registry.molgenis.org"
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
- variable: molgenis.image.tag
|
|
||||||
label: Version
|
|
||||||
default: ""
|
|
||||||
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
- variable: molgenis.adminPassword
|
|
||||||
label: Administrator password
|
|
||||||
default: ""
|
|
||||||
description: "Enter an administrator password"
|
|
||||||
type: password
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
- variable: service.firewall.enabled
|
|
||||||
label: Firewall enabled
|
|
||||||
default: false
|
|
||||||
description: "Firewall enabled (can be cluster or UMCG scoped)"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
show_subquestion_if: true
|
|
||||||
subquestions:
|
|
||||||
- variable: service.firewall.kind
|
|
||||||
default: "umcg"
|
|
||||||
description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
|
|
||||||
type: enum
|
|
||||||
required: true
|
|
||||||
options:
|
|
||||||
- umcg
|
|
||||||
- cluster
|
|
||||||
label: Firewall kind
|
|
||||||
- variable: molgenis.services.opencpu.host
|
|
||||||
label: OpenCPU cluster
|
|
||||||
default: "localhost"
|
|
||||||
description: "Specify the OpenCPU cluster"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
- variable: molgenis.services.postgres.embedded
|
|
||||||
label: Postgres embedded
|
|
||||||
default: false
|
|
||||||
description: "Do you want an embedded postgres"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
show_subquestion_if: false
|
|
||||||
subquestions:
|
|
||||||
- variable: molgenis.services.postgres.host
|
|
||||||
label: Postgres cluster location
|
|
||||||
default: ""
|
|
||||||
description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
- variable: molgenis.services.postgres.scheme
|
|
||||||
label: Database scheme
|
|
||||||
default: "molgenis"
|
|
||||||
description: "Set the database scheme"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
- variable: molgenis.services.postgres.user
|
|
||||||
label: Database username
|
|
||||||
default: "molgenis"
|
|
||||||
description: "Set user of the database scheme"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
- variable: molgenis.services.postgres.password
|
|
||||||
label: Database password
|
|
||||||
default: "molgenis"
|
|
||||||
description: "Set the password of the database scheme"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
- variable: molgenis.resources.limits.memory
|
|
||||||
label: Container memory limit
|
|
||||||
default: 1250Mi
|
|
||||||
description: "Memory limit for this MOLGENIS container"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "1250Mi"
|
|
||||||
- "2500Mi"
|
|
||||||
required: true
|
|
||||||
group: "Resources"
|
|
||||||
- variable: molgenis.resources.requests.memory
|
|
||||||
label: Container memory reservation
|
|
||||||
default: 1250Mi
|
|
||||||
description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "1250Mi"
|
|
||||||
- "2500Mi"
|
|
||||||
required: true
|
|
||||||
group: "Resources"
|
|
||||||
- variable: molgenis.javaOpts.maxHeapSpace
|
|
||||||
label: Maximum heap space (JVM)
|
|
||||||
default: "1g"
|
|
||||||
description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "1g"
|
|
||||||
- "2g"
|
|
||||||
group: "Resources"
|
|
||||||
- variable: persistence.enabled
|
|
||||||
default: true
|
|
||||||
description: "Do you want to use persistence"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Persistence"
|
|
||||||
label: Persistence
|
|
||||||
show_subquestion_if: true
|
|
||||||
subquestions:
|
|
||||||
- variable: persistence.retain
|
|
||||||
default: false
|
|
||||||
description: "Do you want to retain the persistent volume"
|
|
||||||
type: boolean
|
|
||||||
label: Retain volume
|
|
||||||
- variable: molgenis.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "20Gi"
|
|
||||||
label: Size MOLGENIS filestore
|
|
||||||
- variable: elasticsearch.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "50Gi"
|
|
||||||
label: Size for ElasticSearch data
|
|
||||||
- variable: postgres.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of PostgreSQL data (directory that is persist: /var/lib/postgresql/data/pgdata)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "50Gi"
|
|
||||||
label: Size for PostgreSQL data
|
|
||||||
@ -1,19 +0,0 @@
|
|||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.elasticsearch.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
@ -1,19 +0,0 @@
|
|||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.molgenis.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.molgenis.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
@ -1,21 +0,0 @@
|
|||||||
{{- if .Values.molgenis.services.postgres.embedded }}
|
|
||||||
{{- if .Values.persistence.enabled }}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.postgres.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.postgres.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
@ -1,103 +0,0 @@
|
|||||||
# Default values for molgenis.
|
|
||||||
|
|
||||||
replicaCount: 1
|
|
||||||
|
|
||||||
service:
|
|
||||||
type: LoadBalancer
|
|
||||||
firewall:
|
|
||||||
enabled: false
|
|
||||||
kind: "umcg"
|
|
||||||
umcg:
|
|
||||||
rules:
|
|
||||||
- 127.0.0.1/32
|
|
||||||
cluster:
|
|
||||||
rules:
|
|
||||||
- 127.0.0.1/32
|
|
||||||
port: 8080
|
|
||||||
|
|
||||||
ingress:
|
|
||||||
enabled: true
|
|
||||||
annotations:
|
|
||||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
|
||||||
path: /
|
|
||||||
hosts:
|
|
||||||
- name: test.molgenis.org
|
|
||||||
tls: []
|
|
||||||
|
|
||||||
molgenis:
|
|
||||||
image:
|
|
||||||
repository: registry.hub.docker.com
|
|
||||||
name: molgenis/molgenis-app
|
|
||||||
tag: stable
|
|
||||||
pullPolicy: Always
|
|
||||||
adminPassword:
|
|
||||||
javaOpts:
|
|
||||||
maxHeapSpace: "1g"
|
|
||||||
resources:
|
|
||||||
limits:
|
|
||||||
cpu: 1
|
|
||||||
memory: 1250Mi
|
|
||||||
requests:
|
|
||||||
cpu: 200m
|
|
||||||
memory: 1250Mi
|
|
||||||
persistence:
|
|
||||||
claim: molgenis-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
services:
|
|
||||||
opencpu:
|
|
||||||
host: localhost
|
|
||||||
elasticsearch:
|
|
||||||
transportAddresses: localhost:9300
|
|
||||||
clusterName: molgenis
|
|
||||||
postgres:
|
|
||||||
embedded: false
|
|
||||||
host: localhost
|
|
||||||
scheme: molgenis
|
|
||||||
user: molgenis
|
|
||||||
password: molgenis
|
|
||||||
|
|
||||||
elasticsearch:
|
|
||||||
image:
|
|
||||||
repository: docker.elastic.co/elasticsearch/elasticsearch
|
|
||||||
tag: 5.5.3
|
|
||||||
pullPolicy: IfNotPresent
|
|
||||||
javaOpts: "-Xms1g -Xmx1g"
|
|
||||||
clusterName: molgenis
|
|
||||||
resources:
|
|
||||||
limits:
|
|
||||||
cpu: 2
|
|
||||||
memory: 3Gi
|
|
||||||
requests:
|
|
||||||
cpu: 100m
|
|
||||||
memory: 1Gi
|
|
||||||
persistence:
|
|
||||||
claim: elasticsearch-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
|
|
||||||
postgres:
|
|
||||||
image:
|
|
||||||
repository: postgres
|
|
||||||
tag: 9.6-alpine
|
|
||||||
pullPolicy: IfNotPresent
|
|
||||||
resources:
|
|
||||||
limits:
|
|
||||||
cpu: 1
|
|
||||||
memory: 250Mi
|
|
||||||
requests:
|
|
||||||
cpu: 100m
|
|
||||||
memory: 250Mi
|
|
||||||
persistence:
|
|
||||||
claim: postgres-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
|
|
||||||
persistence:
|
|
||||||
enabled: true
|
|
||||||
retain: false
|
|
||||||
|
|
||||||
nodeSelector: {
|
|
||||||
deployPod: "true"
|
|
||||||
}
|
|
||||||
|
|
||||||
tolerations: []
|
|
||||||
|
|
||||||
affinity: {}
|
|
||||||
@ -6,7 +6,3 @@ version: 0.1.0
|
|||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
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
|
|
||||||
|
Before Width: | Height: | Size: 89 KiB After Width: | Height: | Size: 89 KiB |
@ -1,11 +1,8 @@
|
|||||||
name: molgenis-jenkins
|
name: molgenis-jenkins
|
||||||
home: https://jenkins.io/
|
home: https://jenkins.io/
|
||||||
version: 0.8.1
|
version: 0.7.0
|
||||||
appVersion: 2.138.1
|
appVersion: 2.121
|
||||||
description: Molgenis installation for the jenkins chart.
|
description: Molgenis installation for the jenkins chart.
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg
|
||||||
maintainers:
|
|
||||||
- name: fdlk
|
|
||||||
- name: sidohaakma
|
|
||||||
106
molgenis-jenkins/README.md
Normal file
106
molgenis-jenkins/README.md
Normal file
@ -0,0 +1,106 @@
|
|||||||
|
# Molgenis Jenkins Helm Chart
|
||||||
|
|
||||||
|
Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin.
|
||||||
|
Wraps [the kuberenetes jenkins chart](https://github.com/kubernetes/charts/tree/master/stable/jenkins), see documentation there!
|
||||||
|
|
||||||
|
## Chart Details
|
||||||
|
|
||||||
|
This chart will do the following:
|
||||||
|
|
||||||
|
* 1 x Jenkins Master with port 8080 exposed on an external ClusterIP
|
||||||
|
* All using Kubernetes Deployments
|
||||||
|
|
||||||
|
## Installing the Chart
|
||||||
|
|
||||||
|
Usually, you'll be deploying this to the molgenis cluster.
|
||||||
|
In the [Rancher Catalog](https://rancher.molgenis.org:7443/g/catalog), add the latest version of this repository.
|
||||||
|
In the [molgenis cluster management page](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/apps), choose the
|
||||||
|
catalog, pick the molgenis-jenkins app from the catalog and deploy it.
|
||||||
|
|
||||||
|
## Configuration
|
||||||
|
|
||||||
|
When deploying, you can paste values into the Rancher Answers to override the defaults in this chart.
|
||||||
|
Array values can be added as {value, value, value}.
|
||||||
|
```
|
||||||
|
jenkins.Master.HostName=jenkins.molgenis.org
|
||||||
|
jenkins.Master.AdminPassword=pa$$word
|
||||||
|
jenkins.Persistence.Enabled=false
|
||||||
|
jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29}
|
||||||
|
jenkins.Master.Security.UseGitHub=false
|
||||||
|
## if UseGitHub=true
|
||||||
|
jenkins.Master.Security.GitHub.ClientID=id
|
||||||
|
jenkins.Master.Security.GitHub.ClientSecret=S3cr3t
|
||||||
|
## end UseGitHub=true
|
||||||
|
PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
|
||||||
|
```
|
||||||
|
|
||||||
|
You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
|
||||||
|
> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
|
||||||
|
|
||||||
|
### GitHub Authentication delegation
|
||||||
|
You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
|
||||||
|
|
||||||
|
### Additional configuration
|
||||||
|
There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
|
||||||
|
|
||||||
|
* PipelineSecrets
|
||||||
|
|
||||||
|
When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
|
||||||
|
build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
|
||||||
|
each other with their own secrets.
|
||||||
|
|
||||||
|
You can override the values at deploy time but otherwise also configure them
|
||||||
|
[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
|
||||||
|
|
||||||
|
* Vault
|
||||||
|
|
||||||
|
New vault token to be used by the pods to retrieve their tokens from the vault.
|
||||||
|
|
||||||
|
| Parameter | Description | Default |
|
||||||
|
| ----------------------------------|--------------------------------------------|-----------------------------------------------|
|
||||||
|
| `PipelineSecrets.Vault.Replace` | Replace the molgenis-pipeline-vault secret |`true` |
|
||||||
|
| `PipelineSecrets.Vault.Token` | Token to log into the hashicorp vault |`xxxx` |
|
||||||
|
| `PipelineSecrets.Vault.Addr` | Address of the vault |`https:vault-operator.vault-operator.svc:8200` |
|
||||||
|
| `PipelineSecrets.Vault.skipVerify`| Skip verification of the https connection |`1` |
|
||||||
|
|
||||||
|
* Env
|
||||||
|
|
||||||
|
Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
|
||||||
|
in the slave pods.
|
||||||
|
|
||||||
|
| Parameter | Description | Default |
|
||||||
|
| -------------------------------------- | ----------------------------------------- | --------------- |
|
||||||
|
| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
|
||||||
|
| `PipelineSecrets.Env.PGPPassphrase` | passphrase for the pgp signing key | `literal:xxxx` |
|
||||||
|
| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.NexusPassword` | token for molgenis-jenkins user in NEXUS | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.DockerHubPassword`| token for molgenis user in hub.docker.com | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.NpmToken` | token for npmjs.org | `xxxx` |
|
||||||
|
| `PipelineSecrets.Env.SauceAccessKey` | token for saucelabs.com | `xxxx` |
|
||||||
|
|
||||||
|
* File
|
||||||
|
|
||||||
|
Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
|
||||||
|
in the `/root/.m2` directory of the slave pods.
|
||||||
|
> The settings.xml file references the
|
||||||
|
|
||||||
|
| Parameter | Description | Default |
|
||||||
|
| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
|
||||||
|
| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
|
||||||
|
| `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
|
||||||
|
| `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml)) |
|
||||||
|
|
||||||
|
## Command line use
|
||||||
|
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
||||||
|
|
||||||
|
Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart.
|
||||||
|
For example,
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ helm install --name jenkins -f values.yaml molgenis-jenkins
|
||||||
|
```
|
||||||
|
|
||||||
|
> **Tip**: You can use the default [values.yaml](values.yaml)
|
||||||
|
|
||||||
|
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:
|
dependencies:
|
||||||
- name: jenkins
|
- name: jenkins
|
||||||
repository: https://kubernetes-charts.storage.googleapis.com/
|
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||||
version: 0.18.0
|
version: 0.16.4
|
||||||
digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
|
digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
|
||||||
generated: 2018-09-27T11:00:15.795416984+02:00
|
generated: 2018-06-27T14:36:23.172954738+02:00
|
||||||
@ -32,9 +32,6 @@ data:
|
|||||||
<buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
|
<buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
|
||||||
<markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
|
<markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
|
||||||
<jdks/>
|
<jdks/>
|
||||||
<primaryView>dev</primaryView>
|
|
||||||
<viewsTabBar class="hudson.views.DefaultViewsTabBar"/>
|
|
||||||
<myViewsTabBar class="hudson.views.DefaultMyViewsTabBar"/>
|
|
||||||
<clouds>
|
<clouds>
|
||||||
<org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud plugin="kubernetes@{{ template "jenkins.kubernetes-version" . }}">
|
<org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud plugin="kubernetes@{{ template "jenkins.kubernetes-version" . }}">
|
||||||
<name>kubernetes</name>
|
<name>kubernetes</name>
|
||||||
@ -155,8 +152,6 @@ data:
|
|||||||
<readTimeout>0</readTimeout>
|
<readTimeout>0</readTimeout>
|
||||||
</org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud>
|
</org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud>
|
||||||
</clouds>
|
</clouds>
|
||||||
<quietPeriod>5</quietPeriod>
|
|
||||||
<scmCheckoutRetryCount>0</scmCheckoutRetryCount>
|
|
||||||
<views>
|
<views>
|
||||||
<hudson.model.AllView>
|
<hudson.model.AllView>
|
||||||
<owner class="hudson" reference="../../.."/>
|
<owner class="hudson" reference="../../.."/>
|
||||||
@ -194,6 +189,8 @@ data:
|
|||||||
{{- end }}
|
{{- end }}
|
||||||
</views>
|
</views>
|
||||||
<primaryView>{{ .Values.Master.DefaultView }}</primaryView>
|
<primaryView>{{ .Values.Master.DefaultView }}</primaryView>
|
||||||
|
<quietPeriod>5</quietPeriod>
|
||||||
|
<scmCheckoutRetryCount>0</scmCheckoutRetryCount>
|
||||||
<slaveAgentPort>50000</slaveAgentPort>
|
<slaveAgentPort>50000</slaveAgentPort>
|
||||||
<disabledAgentProtocols>
|
<disabledAgentProtocols>
|
||||||
{{- range .Values.Master.DisabledAgentProtocols }}
|
{{- range .Values.Master.DisabledAgentProtocols }}
|
||||||
@ -8,9 +8,9 @@ metadata:
|
|||||||
"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
|
"jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
username: {{ "molgenisci" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
|
||||||
@ -8,9 +8,9 @@ metadata:
|
|||||||
"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
|
"jenkins.io/credentials-description" : "oauth token for the molgenis-jenkins github user"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gitHub.user | b64enc | quote }}
|
username: {{ "molgenis-jenkins" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gitHub.token | b64enc | quote }}
|
password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
|
||||||
@ -8,9 +8,9 @@ metadata:
|
|||||||
"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
|
"jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gogs.user | b64enc | quote }}
|
username: {{ "p281392" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gogs.token | b64enc | quote }}
|
password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
|
||||||
@ -0,0 +1,16 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
|
name: "molgenis-jenkins-nexus-secret"
|
||||||
|
labels:
|
||||||
|
# so we know what type it is.
|
||||||
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
|
annotations: {
|
||||||
|
# description - can not be a label as spaces are not allowed
|
||||||
|
"jenkins.io/credentials-description" : "user to authenticate against NEXUS"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "admin" | b64enc | quote }}
|
||||||
|
password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}
|
||||||
@ -0,0 +1,16 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
|
name: "molgenis-jenkins-saucelabs-secret"
|
||||||
|
labels:
|
||||||
|
# so we know what type it is.
|
||||||
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
|
annotations: {
|
||||||
|
# description - can not be a label as spaces are not allowed
|
||||||
|
"jenkins.io/credentials-description" : "user to authenticate against Saucelabs (saucelabs.com)"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "molgenis-jenkins" | b64enc | quote }}
|
||||||
|
password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}
|
||||||
18
molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml
Normal file
18
molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.Env.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-env-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
|
||||||
|
codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
|
||||||
|
githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
|
||||||
|
sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
|
||||||
|
npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
@ -0,0 +1,15 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.File.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-file-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
|
||||||
|
settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
@ -1,3 +1,4 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.Vault.Replace }}
|
||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
kind: Secret
|
kind: Secret
|
||||||
metadata:
|
metadata:
|
||||||
@ -9,6 +10,7 @@ metadata:
|
|||||||
heritage: "{{ .Release.Service }}"
|
heritage: "{{ .Release.Service }}"
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
token: {{ .Values.secret.vault.token | b64enc | quote }}
|
token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
|
||||||
addr: {{ .Values.secret.vault.addr | b64enc | quote }}
|
addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
|
||||||
skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
|
skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
@ -3,18 +3,16 @@ jenkins:
|
|||||||
HostName: jenkins.molgenis.org
|
HostName: jenkins.molgenis.org
|
||||||
ServiceType: ClusterIP
|
ServiceType: ClusterIP
|
||||||
InstallPlugins:
|
InstallPlugins:
|
||||||
- kubernetes:1.12.6
|
- kubernetes:1.12.3
|
||||||
- workflow-aggregator:2.5
|
- workflow-aggregator:2.5
|
||||||
- workflow-job:2.25
|
- workflow-job:2.24
|
||||||
- credentials-binding:1.16
|
- credentials-binding:1.16
|
||||||
- git:3.9.1
|
- git:3.9.1
|
||||||
- github-branch-source:2.3.6
|
- github-branch-source:2.3.6
|
||||||
- kubernetes-credentials-provider:0.10
|
- kubernetes-credentials-provider:0.9
|
||||||
- blueocean:1.8.3
|
- blueocean:1.8.2
|
||||||
- github-oauth:0.29
|
- github-oauth:0.29
|
||||||
- gogs-webhook:1.0.14
|
- gogs-webhook:1.0.14
|
||||||
- github-scm-trait-commit-skip:0.1.1
|
|
||||||
- slack:2.3
|
|
||||||
Security:
|
Security:
|
||||||
UseGitHub: false
|
UseGitHub: false
|
||||||
GitHub:
|
GitHub:
|
||||||
@ -83,18 +81,6 @@ jenkins:
|
|||||||
<strategyId>1</strategyId>
|
<strategyId>1</strategyId>
|
||||||
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
||||||
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
</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>
|
</traits>
|
||||||
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
||||||
</navigators>
|
</navigators>
|
||||||
@ -144,17 +130,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@ -208,17 +183,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@ -272,17 +236,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@ -336,17 +289,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@ -400,17 +342,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@ -436,8 +367,8 @@ jenkins:
|
|||||||
install: true
|
install: true
|
||||||
Pods:
|
Pods:
|
||||||
molgenis:
|
molgenis:
|
||||||
Label: molgenis
|
Label: molgenisv2
|
||||||
NodeUsageMode: NORMAL
|
NodeUsageMode: EXCLUSIVE
|
||||||
volumes:
|
volumes:
|
||||||
- type: HostPath
|
- type: HostPath
|
||||||
hostPath: "/var/run/docker.sock"
|
hostPath: "/var/run/docker.sock"
|
||||||
@ -484,12 +415,39 @@ jenkins:
|
|||||||
key: VAULT_ADDR
|
key: VAULT_ADDR
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-vault-secret
|
||||||
secretKey: addr
|
secretKey: addr
|
||||||
helm:
|
NodeSelector: {}
|
||||||
Image: "lachlanevenson/k8s-helm"
|
molgenis-legacy:
|
||||||
ImageTag: "v2.10.0"
|
InheritFrom: molgenis
|
||||||
Command: cat
|
Label: molgenis
|
||||||
WorkingDir: /home/jenkins
|
NodeUsageMode: NORMAL
|
||||||
TTY: true
|
volumes:
|
||||||
|
- type: Secret
|
||||||
|
secretName: molgenis-pipeline-file-secret
|
||||||
|
mountPath: "/home/jenkins/.m2"
|
||||||
|
Containers:
|
||||||
|
EnvVars:
|
||||||
|
- type: Secret
|
||||||
|
key: PGP_PASSPHRASE
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: pgpPassphrase
|
||||||
|
- type: KeyValue
|
||||||
|
key: PGP_SECRETKEY
|
||||||
|
value: "keyfile:/home.jenkins/.m2/key.asc"
|
||||||
|
- type: KeyValue
|
||||||
|
key: npm_config_registry
|
||||||
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
|
- type: Secret
|
||||||
|
key: SONAR_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: sonarToken
|
||||||
|
- type: Secret
|
||||||
|
key: CODECOV_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: codecovToken
|
||||||
|
- type: Secret
|
||||||
|
key: GITHUB_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: githubToken
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
node:
|
node:
|
||||||
Label: node-carbon
|
Label: node-carbon
|
||||||
@ -502,24 +460,22 @@ jenkins:
|
|||||||
Command: cat
|
Command: cat
|
||||||
WorkingDir: /home/jenkins
|
WorkingDir: /home/jenkins
|
||||||
TTY: true
|
TTY: true
|
||||||
vault:
|
|
||||||
Image: "vault"
|
|
||||||
Command: cat
|
|
||||||
WorkingDir: /home/jenkins
|
|
||||||
TTY: true
|
|
||||||
EnvVars:
|
EnvVars:
|
||||||
|
- type: KeyValue
|
||||||
|
key: npm_config_registry
|
||||||
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_TOKEN
|
key: CODECOV_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: token
|
secretKey: codecovToken
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_SKIP_VERIFY
|
key: GITHUB_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: skipVerify
|
secretKey: githubToken
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_ADDR
|
key: NPM_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: addr
|
secretKey: npmToken
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
molgenis-it:
|
molgenis-it:
|
||||||
InheritFrom: molgenis
|
InheritFrom: molgenis
|
||||||
@ -583,61 +539,77 @@ jenkins:
|
|||||||
cpu: "1"
|
cpu: "1"
|
||||||
memory: "512Mi"
|
memory: "512Mi"
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
helm:
|
PipelineSecrets:
|
||||||
Label: helm
|
Vault:
|
||||||
NodeUsageMode: EXCLUSIVE
|
Replace: true
|
||||||
Containers:
|
Token: xxxx
|
||||||
chart-testing:
|
Addr: "https://vault-operator.vault-operator.svc:8200"
|
||||||
Image: "quay.io/helmpack/chart-testing"
|
SkipVerify: 1
|
||||||
ImageTag: v1.1.0
|
Env:
|
||||||
Command: cat
|
# Set to false to keep existing secret
|
||||||
WorkingDir: /home/jenkins
|
Replace: true
|
||||||
TTY: true
|
# Passphrase for the pgp private key file, prefixed with literal:
|
||||||
alpine:
|
PGPPassphrase: literal:xxxx
|
||||||
Image: "spotify/alpine"
|
# Token for codecov.io service
|
||||||
Command: cat
|
CodecovToken: xxxx
|
||||||
WorkingDir: /home/jenkins
|
# Token for github bot account
|
||||||
TTY: true
|
GitHubToken: xxxx
|
||||||
vault:
|
# Token for github bot account
|
||||||
Image: "vault"
|
GogsToken: xxxx
|
||||||
Command: cat
|
# Token for sonarcloud.io
|
||||||
WorkingDir: /home/jenkins
|
SonarToken: xxxx
|
||||||
TTY: true
|
# Token for npmjs.org
|
||||||
EnvVars:
|
NpmToken: xxxx
|
||||||
- type: Secret
|
# Password Local NEXUS
|
||||||
key: VAULT_TOKEN
|
NexusPassword: xxxx
|
||||||
secretName: molgenis-pipeline-vault-secret
|
# Password hub.docker.com
|
||||||
secretKey: token
|
DockerHubPassword: xxxx
|
||||||
- type: Secret
|
# Access key for saucelabs.com
|
||||||
key: VAULT_SKIP_VERIFY
|
SauceAccessKey: xxxx
|
||||||
secretName: molgenis-pipeline-vault-secret
|
File:
|
||||||
secretKey: skipVerify
|
# Set to false to keep existing secret
|
||||||
- type: Secret
|
Replace: true
|
||||||
key: VAULT_ADDR
|
# PGP Private key in ascii format used to sign artifacts
|
||||||
secretName: molgenis-pipeline-vault-secret
|
PGPPrivateKeyAsc: |-
|
||||||
secretKey: addr
|
-----BEGIN PGP PRIVATE KEY BLOCK-----
|
||||||
NodeSelector: {}
|
xxxxx
|
||||||
|
-----END PGP PRIVATE KEY BLOCK-----
|
||||||
# secret contains configuration for the kubernetes secrets that jenkins can access
|
# maven.settings file
|
||||||
secret:
|
MavenSettingsXML: |-
|
||||||
# vault configures the vault secret
|
<settings>
|
||||||
vault:
|
<localRepository>${user.home}/.mvnrepository</localRepository>
|
||||||
token: xxxx
|
<interactiveMode>false</interactiveMode>
|
||||||
addr: "https://vault-operator.vault-operator.svc:8200"
|
<mirrors>
|
||||||
skipVerify: "1"
|
<mirror>
|
||||||
# githubToken contains access token for jenkins bot account on github.com
|
<id>nexus</id>
|
||||||
gitHub:
|
<mirrorOf>external:*</mirrorOf>
|
||||||
user: "molgenis-jenkins"
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
|
||||||
token: xxxx
|
</mirror>
|
||||||
# gogs contains access token for jenkins bot account on RuG GoGs
|
</mirrors>
|
||||||
gogs:
|
<servers>
|
||||||
user: p281392
|
<!-- for snapshot builds of the master -->
|
||||||
token: xxxx
|
<server>
|
||||||
# registry contains credentials for registry.molgenis.org
|
<id>sonatype-nexus-staging</id>
|
||||||
registry:
|
<username>molgenis</username>
|
||||||
user: admin
|
<password>xxxx</password>
|
||||||
password: xxxx
|
</server>
|
||||||
# dockerHubPassword contains password for hub.docker.com
|
<server>
|
||||||
dockerHub:
|
<id>local-nexus</id>
|
||||||
user: molgenisci
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
|
||||||
password: xxxx
|
<username>admin</username>
|
||||||
|
<password>xxxxx</password>
|
||||||
|
</server>
|
||||||
|
<!-- for docker images-->
|
||||||
|
<server>
|
||||||
|
<id>registry.molgenis.org</id>
|
||||||
|
<username>admin</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
<!-- to authenticate against GOGS for MAVEN release -->
|
||||||
|
<server>
|
||||||
|
<id>gogs</id>
|
||||||
|
<username>xxxx</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
</servers>
|
||||||
|
</settings>
|
||||||
@ -2,11 +2,7 @@ apiVersion: v1
|
|||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: Nexus stack for MOLGENIS
|
description: Nexus stack for MOLGENIS
|
||||||
name: molgenis-nexus
|
name: molgenis-nexus
|
||||||
version: 0.4.2
|
version: 0.3.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
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
|
|
||||||
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 }}
|
app: {{ .Values.nexus.name }}
|
||||||
creationTimestamp: null
|
creationTimestamp: null
|
||||||
spec:
|
spec:
|
||||||
|
volumes:
|
||||||
|
- name: {{ .Values.persistence.name }}
|
||||||
|
persistentVolumeClaim:
|
||||||
|
claimName: {{ .Values.persistence.name }}
|
||||||
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
||||||
initContainers:
|
initContainers:
|
||||||
- name: nexus-nfs
|
- name: volume-mount-nexus
|
||||||
image: busybox
|
image: busybox
|
||||||
command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
|
command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
|
||||||
volumeMounts:
|
volumeMounts:
|
||||||
- name: molgenis-nexus-nfs
|
- name: {{ .Values.persistence.name }}
|
||||||
mountPath: "/nexus-data"
|
mountPath: "{{ .Values.persistence.mountPath }}"
|
||||||
containers:
|
containers:
|
||||||
- name: {{ .Values.nexus.name }}
|
- name: {{ .Values.nexus.name }}
|
||||||
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
||||||
@ -35,31 +39,6 @@ spec:
|
|||||||
- containerPort: {{ .Values.nexus.port.ui }}
|
- containerPort: {{ .Values.nexus.port.ui }}
|
||||||
- containerPort: {{ .Values.nexus.port.docker }}
|
- containerPort: {{ .Values.nexus.port.docker }}
|
||||||
volumeMounts:
|
volumeMounts:
|
||||||
- name: molgenis-nexus-nfs
|
- name: {{ .Values.persistence.name }}
|
||||||
mountPath: /nexus-data
|
mountPath: "/nexus-data"
|
||||||
livenessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.nexus.port.ui }}
|
|
||||||
initialDelaySeconds: 120
|
|
||||||
periodSeconds: 20
|
|
||||||
failureThreshold: 15
|
|
||||||
successThreshold: 1
|
|
||||||
readinessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.nexus.port.ui }}
|
|
||||||
initialDelaySeconds: 120
|
|
||||||
periodSeconds: 20
|
|
||||||
failureThreshold: 15
|
|
||||||
successThreshold: 1
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
- name: molgenis-nexus-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.persistence.claim }}
|
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
|
||||||
nodeSelector:
|
|
||||||
{{ toYaml . | indent 8 }}
|
|
||||||
{{- end }}
|
|
||||||
@ -5,7 +5,7 @@ kind: Ingress
|
|||||||
metadata:
|
metadata:
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
name: "{{ $.Release.Name }}-ingress"
|
||||||
labels:
|
labels:
|
||||||
app: {{ $.Values.nexusProxy.name }}
|
app: httpd
|
||||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
||||||
release: "{{ $.Release.Name }}"
|
release: "{{ $.Release.Name }}"
|
||||||
heritage: "{{ $.Release.Service }}"
|
heritage: "{{ $.Release.Service }}"
|
||||||
@ -25,8 +25,8 @@ spec:
|
|||||||
paths:
|
paths:
|
||||||
- path: {{ default "/" .path }}
|
- path: {{ default "/" .path }}
|
||||||
backend:
|
backend:
|
||||||
serviceName: {{ $.Values.nexusProxy.name }}
|
serviceName: httpd
|
||||||
servicePort: {{ $.Values.nexusProxy.port }}
|
servicePort: 80
|
||||||
{{- if .tls }}
|
{{- if .tls }}
|
||||||
tls:
|
tls:
|
||||||
- hosts:
|
- 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: {}
|
||||||
@ -1,12 +1,8 @@
|
|||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: MOLGENIS - helm stack (in BETA)
|
description: A Helm chart for Kubernetes
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: 0.4.3
|
version: 0.2.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
|
||||||
home: http://molgenis.org
|
|
||||||
maintainers:
|
|
||||||
- name: sidohaakma
|
|
||||||
- name: fdlk
|
|
||||||
11
molgenis-preview/README.md
Normal file
11
molgenis-preview/README.md
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
# MOLGENIS preview
|
||||||
|
Is used for integration testing purposes.
|
||||||
|
|
||||||
|
## Containers
|
||||||
|
This chart spins up a complete stack to run MOLGENIS. The created containers are:
|
||||||
|
|
||||||
|
- MOLGENIS
|
||||||
|
- PostgreSQL
|
||||||
|
- Elasticsearch
|
||||||
|
- OpenCPU
|
||||||
|
|
||||||
|
Before Width: | Height: | Size: 77 KiB After Width: | Height: | Size: 77 KiB |
44
molgenis-preview/questions.yml
Normal file
44
molgenis-preview/questions.yml
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
|
||||||
|
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.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
|
||||||
@ -17,8 +17,6 @@ spec:
|
|||||||
matchLabels:
|
matchLabels:
|
||||||
app: {{ template "molgenis.name" . }}
|
app: {{ template "molgenis.name" . }}
|
||||||
release: {{ .Release.Name }}
|
release: {{ .Release.Name }}
|
||||||
strategy:
|
|
||||||
type: Recreate
|
|
||||||
template:
|
template:
|
||||||
metadata:
|
metadata:
|
||||||
labels:
|
labels:
|
||||||
@ -28,50 +26,37 @@ spec:
|
|||||||
containers:
|
containers:
|
||||||
- name: molgenis
|
- name: molgenis
|
||||||
{{- with .Values.molgenis }}
|
{{- with .Values.molgenis }}
|
||||||
image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
imagePullPolicy: {{ .image.pullPolicy }}
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
env:
|
env:
|
||||||
- name: molgenis.home
|
- name: molgenis.home
|
||||||
value: /home/molgenis
|
value: /home/molgenis
|
||||||
- name: opencpu.uri.host
|
- name: opencpu.uri.host
|
||||||
value: {{ .services.opencpu.host }}
|
value: localhost
|
||||||
- name: elasticsearch.transport.addresses
|
- name: elasticsearch.transport.addresses
|
||||||
value: {{ .services.elasticsearch.transportAddresses }}
|
value: localhost:9300
|
||||||
- name: elasticsearch.cluster.name
|
- name: elasticsearch.cluster.name
|
||||||
value: {{ .services.elasticsearch.clusterName }}
|
value: {{ $.Values.elasticsearch.clusterName }}
|
||||||
- name: db_uri
|
- name: db_uri
|
||||||
value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
|
value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
|
||||||
- name: db_user
|
- name: db_user
|
||||||
value: {{ .services.postgres.user }}
|
value: {{ $.Values.postgres.user }}
|
||||||
- name: db_password
|
- name: db_password
|
||||||
value: {{ .services.postgres.password }}
|
value: {{ $.Values.postgres.password }}
|
||||||
- name: admin.password
|
- name: admin.password
|
||||||
value: {{ .adminPassword }}
|
value: {{ .adminPassword }}
|
||||||
- name: CATALINA_OPTS
|
- name: CATALINA_OPTS
|
||||||
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
value: "{{ .javaOpts }}"
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 8080
|
- containerPort: 8080
|
||||||
{{- if $.Values.persistence.enabled }}
|
# livenessProbe:
|
||||||
volumeMounts:
|
# httpGet:
|
||||||
- name: molgenis-nfs
|
# path: /
|
||||||
mountPath: /home/molgenis
|
# port: 8080
|
||||||
{{- end }}
|
# readinessProbe:
|
||||||
livenessProbe:
|
# httpGet:
|
||||||
httpGet:
|
# path: /api/v2/version
|
||||||
path: /
|
# port: 8080
|
||||||
port: 8080
|
|
||||||
initialDelaySeconds: 60
|
|
||||||
periodSeconds: 5
|
|
||||||
failureThreshold: 25
|
|
||||||
successThreshold: 1
|
|
||||||
readinessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /api/v2/version
|
|
||||||
port: 8080
|
|
||||||
initialDelaySeconds: 120
|
|
||||||
periodSeconds: 30
|
|
||||||
failureThreshold: 3
|
|
||||||
successThreshold: 1
|
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
@ -94,11 +79,6 @@ spec:
|
|||||||
ports:
|
ports:
|
||||||
- containerPort: 9200
|
- containerPort: 9200
|
||||||
- containerPort: 9300
|
- containerPort: 9300
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: elasticsearch-nfs
|
|
||||||
mountPath: /usr/share/elasticsearch/data
|
|
||||||
{{- end }}
|
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
@ -109,34 +89,25 @@ spec:
|
|||||||
imagePullPolicy: {{ .image.pullPolicy }}
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
env:
|
env:
|
||||||
- name: POSTGRES_USER
|
- name: POSTGRES_USER
|
||||||
value: {{ $.Values.molgenis.services.postgres.user }}
|
value: {{ .user }}
|
||||||
- name: POSTGRES_PASSWORD
|
- name: POSTGRES_PASSWORD
|
||||||
value: {{ $.Values.molgenis.services.postgres.password }}
|
value: {{ .password }}
|
||||||
- name: POSTGRES_DB
|
- name: POSTGRES_DB
|
||||||
value: {{ $.Values.molgenis.services.postgres.scheme }}
|
value: {{ .db }}
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 5432
|
- containerPort: 5432
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: postgres-nfs
|
|
||||||
mountPath: /var/lib/postgresql/data
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|
||||||
|
- name: opencpu
|
||||||
{{- if .Values.persistence.enabled }}
|
{{- with .Values.opencpu }}
|
||||||
volumes:
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
- name: molgenis-nfs
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
persistentVolumeClaim:
|
ports:
|
||||||
claimName: {{ .Values.molgenis.persistence.claim }}
|
- containerPort: 8004
|
||||||
- name: elasticsearch-nfs
|
resources:
|
||||||
persistentVolumeClaim:
|
{{ toYaml .resources | indent 12 }}
|
||||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
- name: postgres-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.postgres.persistence.claim }}
|
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
{{- with .Values.nodeSelector }}
|
||||||
@ -4,7 +4,7 @@
|
|||||||
apiVersion: extensions/v1beta1
|
apiVersion: extensions/v1beta1
|
||||||
kind: Ingress
|
kind: Ingress
|
||||||
metadata:
|
metadata:
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
name: {{ $fullName }}
|
||||||
labels:
|
labels:
|
||||||
app: {{ template "molgenis.name" . }}
|
app: {{ template "molgenis.name" . }}
|
||||||
chart: {{ template "molgenis.chart" . }}
|
chart: {{ template "molgenis.chart" . }}
|
||||||
@ -33,6 +33,6 @@ spec:
|
|||||||
- path: {{ $ingressPath }}
|
- path: {{ $ingressPath }}
|
||||||
backend:
|
backend:
|
||||||
serviceName: {{ $fullName }}
|
serviceName: {{ $fullName }}
|
||||||
servicePort: {{ $.Values.service.port }}
|
servicePort: 8080
|
||||||
{{- end }}
|
{{- end }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
@ -9,18 +9,6 @@ metadata:
|
|||||||
heritage: {{ .Release.Service }}
|
heritage: {{ .Release.Service }}
|
||||||
spec:
|
spec:
|
||||||
type: {{ .Values.service.type }}
|
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:
|
ports:
|
||||||
- name: molgenis
|
- name: molgenis
|
||||||
port: {{ .Values.service.port }}
|
port: {{ .Values.service.port }}
|
||||||
120
molgenis-preview/test.yaml
Normal file
120
molgenis-preview/test.yaml
Normal file
@ -0,0 +1,120 @@
|
|||||||
|
# Source: molgenis/templates/deployment.yaml
|
||||||
|
apiVersion: apps/v1beta2
|
||||||
|
kind: Deployment
|
||||||
|
metadata:
|
||||||
|
name: lanky-ragdoll-molgenis
|
||||||
|
labels:
|
||||||
|
app: molgenis
|
||||||
|
chart: molgenis-0.1.0
|
||||||
|
release: lanky-ragdoll
|
||||||
|
heritage: Tiller
|
||||||
|
spec:
|
||||||
|
replicas: 1
|
||||||
|
selector:
|
||||||
|
matchLabels:
|
||||||
|
app: molgenis
|
||||||
|
release: lanky-ragdoll
|
||||||
|
template:
|
||||||
|
metadata:
|
||||||
|
labels:
|
||||||
|
app: molgenis
|
||||||
|
release: lanky-ragdoll
|
||||||
|
spec:
|
||||||
|
containers:
|
||||||
|
- name: molgenis
|
||||||
|
image: "registry.molgenis.org/molgenis/molgenis-app:latest"
|
||||||
|
imagePullPolicy: Always
|
||||||
|
env:
|
||||||
|
- name: molgenis.home
|
||||||
|
value: /home/molgenis
|
||||||
|
- name: opencpu.uri.host
|
||||||
|
value: opencpu
|
||||||
|
- name: elasticsearch.transport.addresses
|
||||||
|
value: elasticsearch:9300
|
||||||
|
- name: elasticsearch.cluster.name
|
||||||
|
value: molgenis
|
||||||
|
- name: db_uri
|
||||||
|
value: "jdbc:postgresql://postgres/molgenis"
|
||||||
|
- name: db_user
|
||||||
|
value: molgenis
|
||||||
|
- name: db_password
|
||||||
|
value: molgenis
|
||||||
|
- name: admin.password
|
||||||
|
value: admin
|
||||||
|
- name: CATALINA_OPTS
|
||||||
|
value: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||||
|
ports:
|
||||||
|
- containerPort: 8080
|
||||||
|
livenessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /
|
||||||
|
port: http
|
||||||
|
readinessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /api/v2/version
|
||||||
|
port: http
|
||||||
|
resources:
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 1250Mi
|
||||||
|
requests:
|
||||||
|
cpu: 200m
|
||||||
|
memory: 1Gi
|
||||||
|
|
||||||
|
|
||||||
|
- name: elasticsearch
|
||||||
|
image: "docker.elastic.co/elasticsearch/elasticsearch:5.5.3"
|
||||||
|
imagePullPolicy: IfNotPresent
|
||||||
|
env:
|
||||||
|
- name: cluster.name
|
||||||
|
value: molgenis
|
||||||
|
- name: bootstrap.memory_lock
|
||||||
|
value: true
|
||||||
|
- name: ES_JAVA_OPTS
|
||||||
|
value: "-Xms512m -Xmx512m"
|
||||||
|
- name: xpack.security.enabled
|
||||||
|
value: false
|
||||||
|
- name: discovery.type
|
||||||
|
value: single-node
|
||||||
|
ports:
|
||||||
|
- containerPort: 9200
|
||||||
|
- containerPort: 9300
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 1500Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 1Gi
|
||||||
|
|
||||||
|
|
||||||
|
- name: postgres
|
||||||
|
image: "postgres:9.6-alpine"
|
||||||
|
imagePullPolicy: IfNotPresent
|
||||||
|
env:
|
||||||
|
- name: POSTGRES_USER
|
||||||
|
value: molgenis
|
||||||
|
- name: POSTGRES_PASSWORD
|
||||||
|
value: molgenis
|
||||||
|
- name: POSTGRES_DB
|
||||||
|
value: molgenis
|
||||||
|
ports:
|
||||||
|
- containerPort: 5432
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 250Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 250Mi
|
||||||
|
|
||||||
|
|
||||||
|
- name: opencpu
|
||||||
|
image: "molgenis/opencpu:latest"
|
||||||
|
imagePullPolicy: Always
|
||||||
|
ports:
|
||||||
|
- containerPort: 8004
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 512Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 256Mi
|
||||||
81
molgenis-preview/values.yaml
Normal file
81
molgenis-preview/values.yaml
Normal file
@ -0,0 +1,81 @@
|
|||||||
|
# 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/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: {}
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user