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@ -25,47 +25,59 @@ Array values can be added as {value, value, value}.
|
||||||
jenkins.Master.HostName=jenkins.molgenis.org
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jenkins.Master.HostName=jenkins.molgenis.org
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jenkins.Master.AdminPassword=pa$$word
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jenkins.Master.AdminPassword=pa$$word
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jenkins.Persistence.Enabled=false
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jenkins.Persistence.Enabled=false
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jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1}
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jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29}
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jenkins.Master.Security.UseGitHub=false
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## if UseGitHub=true
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jenkins.Master.Security.GitHub.ClientID=id
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jenkins.Master.Security.GitHub.ClientSecret=S3cr3t
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||||||
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## end UseGitHub=true
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PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
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PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
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||||||
```
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```
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||||||
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|
||||||
You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
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You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
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||||||
> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
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> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
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||||||
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### GitHub Authentication delegation
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You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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||||||
|
### Additional configuration
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||||||
There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
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There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
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||||||
## PipelineSecrets
|
|
||||||
|
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||||||
When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
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* PipelineSecrets
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||||||
build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
|
|
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each other with their own secrets.
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|
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You can override the values at deploy time but otherwise also configure them
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
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each other with their own secrets.
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|
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### Env
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You can override the values at deploy time but otherwise also configure them
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Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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in the slave pods.
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| Parameter | Description | Default |
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* Env
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||||||
| ---------------------------------- | ------------------------------------ | --------------- |
|
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||||||
| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
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Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
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| `PipelineSecrets.Env.PGPPassphrase`| passphrase for the pgp signing key | `literal:xxxx` |
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in the slave pods.
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| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
|
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| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
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| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` | |
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|
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### File
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| Parameter | Description | Default |
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||||||
|
| -------------------------------------- | ----------------------------------------- | --------------- |
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||||||
|
| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
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||||||
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| `PipelineSecrets.Env.PGPPassphrase` | passphrase for the pgp signing key | `literal:xxxx` |
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| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
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| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
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| `PipelineSecrets.Env.NexusPassword` | token for molgenis-jenkins user in NEXUS | `xxxx` |
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| `PipelineSecrets.Env.DockerHubPassword`| token for molgenis user in hub.docker.com | `xxxx` |
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| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` | |
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||||||
|
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Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
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* File
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||||||
in the `/root/.m2` directory of the slave pods.
|
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||||||
> The settings.xml file references the
|
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
|
||||||
| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
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in the `/root/.m2` directory of the slave pods.
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| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
|
> The settings.xml file references the
|
||||||
| `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
|
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||||||
| `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml)) |
|
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|
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||||||
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| Parameter | Description | Default |
|
||||||
|
| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
|
||||||
|
| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
|
||||||
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| `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
|
## Command line use
|
||||||
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
||||||
|
|
|
@ -15,7 +15,17 @@ data:
|
||||||
<authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
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<authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
|
||||||
<denyAnonymousReadAccess>true</denyAnonymousReadAccess>
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<denyAnonymousReadAccess>true</denyAnonymousReadAccess>
|
||||||
</authorizationStrategy>
|
</authorizationStrategy>
|
||||||
|
{{- if .Values.jenkins.Master.Security.UseGitHub }}
|
||||||
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<securityRealm class="org.jenkinsci.plugins.GithubSecurityRealm">
|
||||||
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<githubWebUri>https://github.com</githubWebUri>
|
||||||
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<githubApiUri>https://api.github.com</githubApiUri>
|
||||||
|
<clientID>{{ .Values.jenkins.Master.Security.Github.ClientID }}</clientID>
|
||||||
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<clientSecret>{{ .Values.jenkins.Master.Security.Github.ClientSecret }}</clientSecret>
|
||||||
|
<oauthScopes>read:org,user:email</oauthScopes>
|
||||||
|
</securityRealm>
|
||||||
|
{{- else }}
|
||||||
<securityRealm class="hudson.security.LegacySecurityRealm"/>
|
<securityRealm class="hudson.security.LegacySecurityRealm"/>
|
||||||
|
{{- end }}
|
||||||
<disableRememberMe>false</disableRememberMe>
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<disableRememberMe>false</disableRememberMe>
|
||||||
<projectNamingStrategy class="jenkins.model.ProjectNamingStrategy$DefaultProjectNamingStrategy"/>
|
<projectNamingStrategy class="jenkins.model.ProjectNamingStrategy$DefaultProjectNamingStrategy"/>
|
||||||
<workspaceDir>${JENKINS_HOME}/workspace/${ITEM_FULLNAME}</workspaceDir>
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<workspaceDir>${JENKINS_HOME}/workspace/${ITEM_FULLNAME}</workspaceDir>
|
||||||
|
|
|
@ -0,0 +1,16 @@
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
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name: "molgenis-jenkins-dockerhub-secret"
|
||||||
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labels:
|
||||||
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# so we know what type it is.
|
||||||
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"jenkins.io/credentials-type": "usernamePassword"
|
||||||
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annotations: {
|
||||||
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# description - can not be a label as spaces are not allowed
|
||||||
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"jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "molgenisci" | b64enc | quote }}
|
||||||
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password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
|
|
@ -10,7 +10,13 @@ jenkins:
|
||||||
- git:3.9.1
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- git:3.9.1
|
||||||
- github-branch-source:2.3.6
|
- github-branch-source:2.3.6
|
||||||
- kubernetes-credentials-provider:0.9
|
- kubernetes-credentials-provider:0.9
|
||||||
- blueocean:1.6.1
|
- blueocean:1.6.2
|
||||||
|
- github-oauth:0.29
|
||||||
|
Security:
|
||||||
|
UseGitHub: false
|
||||||
|
GitHub:
|
||||||
|
ClientID: ""
|
||||||
|
ClienSecret: ""
|
||||||
Jobs: |-
|
Jobs: |-
|
||||||
molgenis: |-
|
molgenis: |-
|
||||||
<?xml version='1.1' encoding='UTF-8'?>
|
<?xml version='1.1' encoding='UTF-8'?>
|
||||||
|
@ -269,6 +275,8 @@ PipelineSecrets:
|
||||||
SonarToken: xxxx
|
SonarToken: xxxx
|
||||||
# Password Local NEXUS
|
# Password Local NEXUS
|
||||||
NexusPassword: xxxx
|
NexusPassword: xxxx
|
||||||
|
# Password hub.docker.com
|
||||||
|
DockerHubPassword: xxxx
|
||||||
File:
|
File:
|
||||||
# Set to false to keep existing secret
|
# Set to false to keep existing secret
|
||||||
Replace: true
|
Replace: true
|
||||||
|
|
|
@ -0,0 +1,21 @@
|
||||||
|
# Patterns to ignore when building packages.
|
||||||
|
# This supports shell glob matching, relative path matching, and
|
||||||
|
# negation (prefixed with !). Only one pattern per line.
|
||||||
|
.DS_Store
|
||||||
|
# Common VCS dirs
|
||||||
|
.git/
|
||||||
|
.gitignore
|
||||||
|
.bzr/
|
||||||
|
.bzrignore
|
||||||
|
.hg/
|
||||||
|
.hgignore
|
||||||
|
.svn/
|
||||||
|
# Common backup files
|
||||||
|
*.swp
|
||||||
|
*.bak
|
||||||
|
*.tmp
|
||||||
|
*~
|
||||||
|
# Various IDEs
|
||||||
|
.project
|
||||||
|
.idea/
|
||||||
|
*.tmproj
|
|
@ -0,0 +1,5 @@
|
||||||
|
apiVersion: v1
|
||||||
|
appVersion: "1.0"
|
||||||
|
description: A Helm chart for Kubernetes
|
||||||
|
name: molgenis
|
||||||
|
version: 0.1.0
|
|
@ -0,0 +1,19 @@
|
||||||
|
1. Get the application URL by running these commands:
|
||||||
|
{{- if .Values.ingress.enabled }}
|
||||||
|
{{- range .Values.ingress.hosts }}
|
||||||
|
http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
|
||||||
|
{{- end }}
|
||||||
|
{{- else if contains "NodePort" .Values.service.type }}
|
||||||
|
export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
|
||||||
|
export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
|
||||||
|
echo http://$NODE_IP:$NODE_PORT
|
||||||
|
{{- else if contains "LoadBalancer" .Values.service.type }}
|
||||||
|
NOTE: It may take a few minutes for the LoadBalancer IP to be available.
|
||||||
|
You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
|
||||||
|
export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
|
||||||
|
echo http://$SERVICE_IP:{{ .Values.service.port }}
|
||||||
|
{{- else if contains "ClusterIP" .Values.service.type }}
|
||||||
|
export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
|
||||||
|
echo "Visit http://127.0.0.1:8080 to use your application"
|
||||||
|
kubectl port-forward $POD_NAME 8080:80
|
||||||
|
{{- end }}
|
|
@ -0,0 +1,32 @@
|
||||||
|
{{/* vim: set filetype=mustache: */}}
|
||||||
|
{{/*
|
||||||
|
Expand the name of the chart.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis.name" -}}
|
||||||
|
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/*
|
||||||
|
Create a default fully qualified app name.
|
||||||
|
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
||||||
|
If release name contains chart name it will be used as a full name.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis.fullname" -}}
|
||||||
|
{{- if .Values.fullnameOverride -}}
|
||||||
|
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- else -}}
|
||||||
|
{{- $name := default .Chart.Name .Values.nameOverride -}}
|
||||||
|
{{- if contains $name .Release.Name -}}
|
||||||
|
{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- else -}}
|
||||||
|
{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
{{- end -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/*
|
||||||
|
Create chart name and version as used by the chart label.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis.chart" -}}
|
||||||
|
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
|
@ -0,0 +1,128 @@
|
||||||
|
apiVersion: apps/v1beta2
|
||||||
|
kind: Deployment
|
||||||
|
metadata:
|
||||||
|
name: {{ template "molgenis.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
spec:
|
||||||
|
replicas: {{ .Values.replicaCount }}
|
||||||
|
selector:
|
||||||
|
matchLabels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
template:
|
||||||
|
metadata:
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
spec:
|
||||||
|
containers:
|
||||||
|
- name: molgenis
|
||||||
|
{{- with .Values.molgenis }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
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: {{ $.Values.elasticsearch.clusterName }}
|
||||||
|
- name: db_uri
|
||||||
|
value: "jdbc:postgresql://postgres/{{ $.Values.postgres.db }}"
|
||||||
|
- name: db_user
|
||||||
|
value: {{ $.Values.postgres.user }}
|
||||||
|
- name: db_password
|
||||||
|
value: {{ $.Values.postgres.password }}
|
||||||
|
- name: admin.password
|
||||||
|
value: {{ .adminPassword }}
|
||||||
|
- name: CATALINA_OPTS
|
||||||
|
value: "{{ .javaOpts }}"
|
||||||
|
ports:
|
||||||
|
- containerPort: 8080
|
||||||
|
command: ["sh"]
|
||||||
|
args: ["-c", "cat"]
|
||||||
|
livenessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /
|
||||||
|
port: http
|
||||||
|
readinessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /api/v2/version
|
||||||
|
port: http
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: elasticsearch
|
||||||
|
{{- with .Values.elasticsearch }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: cluster.name
|
||||||
|
value: {{ .clusterName }}
|
||||||
|
- name: bootstrap.memory_lock
|
||||||
|
value: "true"
|
||||||
|
- name: ES_JAVA_OPTS
|
||||||
|
value: "{{ .javaOpts }}"
|
||||||
|
- name: xpack.security.enabled
|
||||||
|
value: "false"
|
||||||
|
- name: discovery.type
|
||||||
|
value: single-node
|
||||||
|
ports:
|
||||||
|
- containerPort: 9200
|
||||||
|
- containerPort: 9300
|
||||||
|
command: ["sh"]
|
||||||
|
args: ["-c", "cat"]
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: postgres
|
||||||
|
{{- with .Values.postgres }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: POSTGRES_USER
|
||||||
|
value: {{ .user }}
|
||||||
|
- name: POSTGRES_PASSWORD
|
||||||
|
value: {{ .password }}
|
||||||
|
- name: POSTGRES_DB
|
||||||
|
value: {{ .db }}
|
||||||
|
ports:
|
||||||
|
- containerPort: 5432
|
||||||
|
command: ["sh"]
|
||||||
|
args: ["-c", "cat"]
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: opencpu
|
||||||
|
{{- with .Values.opencpu }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
ports:
|
||||||
|
- containerPort: 8004
|
||||||
|
command: ["sh"]
|
||||||
|
args: ["-c", "cat"]
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
{{- with .Values.nodeSelector }}
|
||||||
|
nodeSelector:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
|
{{- with .Values.affinity }}
|
||||||
|
affinity:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
|
{{- with .Values.tolerations }}
|
||||||
|
tolerations:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
|
@ -0,0 +1,38 @@
|
||||||
|
{{- if .Values.ingress.enabled -}}
|
||||||
|
{{- $fullName := include "molgenis.fullname" . -}}
|
||||||
|
{{- $ingressPath := .Values.ingress.path -}}
|
||||||
|
apiVersion: extensions/v1beta1
|
||||||
|
kind: Ingress
|
||||||
|
metadata:
|
||||||
|
name: {{ $fullName }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
{{- with .Values.ingress.annotations }}
|
||||||
|
annotations:
|
||||||
|
{{ toYaml . | indent 4 }}
|
||||||
|
{{- end }}
|
||||||
|
spec:
|
||||||
|
{{- if .Values.ingress.tls }}
|
||||||
|
tls:
|
||||||
|
{{- range .Values.ingress.tls }}
|
||||||
|
- hosts:
|
||||||
|
{{- range .hosts }}
|
||||||
|
- {{ . }}
|
||||||
|
{{- end }}
|
||||||
|
secretName: {{ .secretName }}
|
||||||
|
{{- end }}
|
||||||
|
{{- end }}
|
||||||
|
rules:
|
||||||
|
{{- range .Values.ingress.hosts }}
|
||||||
|
- host: {{ . }}
|
||||||
|
http:
|
||||||
|
paths:
|
||||||
|
- path: {{ $ingressPath }}
|
||||||
|
backend:
|
||||||
|
serviceName: {{ $fullName }}
|
||||||
|
servicePort: http
|
||||||
|
{{- end }}
|
||||||
|
{{- end }}
|
|
@ -0,0 +1,19 @@
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Service
|
||||||
|
metadata:
|
||||||
|
name: {{ template "molgenis.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
spec:
|
||||||
|
type: {{ .Values.service.type }}
|
||||||
|
ports:
|
||||||
|
- port: {{ .Values.service.port }}
|
||||||
|
targetPort: http
|
||||||
|
protocol: TCP
|
||||||
|
name: http
|
||||||
|
selector:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
|
@ -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
|
|
@ -0,0 +1,82 @@
|
||||||
|
# Default values for molgenis.
|
||||||
|
|
||||||
|
replicaCount: 1
|
||||||
|
|
||||||
|
service:
|
||||||
|
type: ClusterIP
|
||||||
|
port: 8080
|
||||||
|
|
||||||
|
ingress:
|
||||||
|
enabled: false
|
||||||
|
annotations: {}
|
||||||
|
# kubernetes.io/ingress.class: nginx
|
||||||
|
# kubernetes.io/tls-acme: "true"
|
||||||
|
path: /
|
||||||
|
hosts:
|
||||||
|
- molgenis.local
|
||||||
|
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: {}
|
Loading…
Reference in New Issue