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15 Commits
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| Author | SHA1 | Date |
|---|---|---|
Fleur Kelpin
|
2a47abaf26 | |
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Fleur Kelpin
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33779bf6b0 | |
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Fleur Kelpin
|
b240f81fd3 | |
|
Fleur Kelpin
|
f976e96c14 | |
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Fleur Kelpin
|
dba4bb3631 | |
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Fleur Kelpin
|
a03ea8a9b1 | |
|
Fleur Kelpin
|
ee809b636d | |
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Fleur Kelpin
|
72ea0f9424 | |
Sido Haakma
|
f94e6da6e3 | |
Fleur Kelpin
|
b73fd578ea | |
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Fleur Kelpin
|
486ab89b41 | |
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Fleur Kelpin
|
d8b8bd9a22 | |
sido
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4e6349dacb | |
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sido
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4312e92860 | |
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sido
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02f7b7de1b |
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@ -0,0 +1,16 @@
|
|||
pipeline {
|
||||
agent {
|
||||
kubernetes {
|
||||
label 'helm'
|
||||
}
|
||||
}
|
||||
stages {
|
||||
stage('Test') {
|
||||
steps {
|
||||
container('chart-testing') {
|
||||
sh "chart_test.sh --no-install --all"
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -6,3 +6,7 @@ version: 0.1.0
|
|||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg
|
||||
home: http://httpd.apache.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
|
Before Width: | Height: | Size: 89 KiB After Width: | Height: | Size: 89 KiB |
|
|
@ -0,0 +1,11 @@
|
|||
name: molgenis-jenkins
|
||||
home: https://jenkins.io/
|
||||
version: 0.7.1
|
||||
appVersion: 2.121
|
||||
description: Molgenis installation for the jenkins chart.
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg
|
||||
maintainers:
|
||||
- name: fdlk
|
||||
- name: sidohaakma
|
||||
|
|
@ -0,0 +1,111 @@
|
|||
# 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` |
|
||||
|
||||
#### 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)
|
||||
|
||||
|
Before Width: | Height: | Size: 133 KiB After Width: | Height: | Size: 133 KiB |
|
|
@ -0,0 +1,6 @@
|
|||
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
|
||||
|
|
@ -0,0 +1,608 @@
|
|||
jenkins:
|
||||
Master:
|
||||
HostName: jenkins.molgenis.org
|
||||
ServiceType: ClusterIP
|
||||
InstallPlugins:
|
||||
- kubernetes:1.12.6
|
||||
- workflow-aggregator:2.5
|
||||
- workflow-job:2.25
|
||||
- credentials-binding:1.16
|
||||
- git:3.9.1
|
||||
- github-branch-source:2.3.6
|
||||
- kubernetes-credentials-provider:0.10
|
||||
- blueocean:1.8.3
|
||||
- github-oauth:0.29
|
||||
- gogs-webhook:1.0.14
|
||||
- github-scm-trait-commit-skip:0.1.1
|
||||
Security:
|
||||
UseGitHub: false
|
||||
GitHub:
|
||||
ClientID: ""
|
||||
ClienSecret: ""
|
||||
DefaultView: dev
|
||||
Views:
|
||||
dev:
|
||||
- molgenis
|
||||
ops:
|
||||
- molgenis-ops-docker-httpd
|
||||
- molgenis-ops-docker-maven
|
||||
- molgenis-ops-docker-node
|
||||
- molgenis-ops-tools
|
||||
- molgenis-ops-tomcat
|
||||
Jobs: |-
|
||||
molgenis: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<jenkins.branch.OrganizationFolder plugin="branch-api@2.0.20">
|
||||
<actions/>
|
||||
<description></description>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
<jenkins.branch.NoTriggerOrganizationFolderProperty>
|
||||
<branches>.*</branches>
|
||||
</jenkins.branch.NoTriggerOrganizationFolderProperty>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.OrganizationFolderViewHolder">
|
||||
<owner reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon">
|
||||
<owner class="jenkins.branch.OrganizationFolder" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers>
|
||||
<com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger plugin="cloudbees-folder@6.5.1">
|
||||
<spec>H H * * *</spec>
|
||||
<interval>86400000</interval>
|
||||
</com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger>
|
||||
</triggers>
|
||||
<disabled>false</disabled>
|
||||
<navigators>
|
||||
<org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator plugin="github-branch-source@2.3.6">
|
||||
<repoOwner>molgenis</repoOwner>
|
||||
<credentialsId>molgenis-jenkins-github-secret</credentialsId>
|
||||
<traits>
|
||||
<org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
</org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
</org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
||||
<strategyId>1</strategyId>
|
||||
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
||||
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
||||
</navigators>
|
||||
<projectFactories>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory plugin="workflow-multibranch@2.19">
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory>
|
||||
</projectFactories>
|
||||
<buildStrategies/>
|
||||
</jenkins.branch.OrganizationFolder>
|
||||
molgenis-ops-docker-httpd: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>HTTPD server that can be used for redirection and proxieing</description>
|
||||
<displayName>molgenis-ops-docker-httpd</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>a756941d-6c9d-4492-bcf9-327041764be6</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-httpd.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-docker-node: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>NodeJS build container with Curl</description>
|
||||
<displayName>molgenis-ops-docker-node</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>a756941d-6c9d-4492-bcf9-327041764be6</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-node.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-docker-maven: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MAVEN build container with RPMbuild and Curl</description>
|
||||
<displayName>molgenis-ops-docker-maven</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-maven.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-tomcat: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MOLGENIS tomcat package to manage tomcat version on CentOS</description>
|
||||
<displayName>molgenis-ops-tomcat</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tomcat.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
molgenis-ops-tools: |-
|
||||
<?xml version='1.1' encoding='UTF-8'?>
|
||||
<org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
|
||||
<actions/>
|
||||
<description>MOLGENIS operations tools-package to configure firewall, apache, sudoers, etc.</description>
|
||||
<displayName>molgenis-ops-tools</displayName>
|
||||
<properties>
|
||||
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
|
||||
<dockerLabel></dockerLabel>
|
||||
<registry plugin="docker-commons@1.13"/>
|
||||
</org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
|
||||
</properties>
|
||||
<folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</folderViews>
|
||||
<healthMetrics>
|
||||
<com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
|
||||
<nonRecursive>false</nonRecursive>
|
||||
</com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
|
||||
</healthMetrics>
|
||||
<icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</icon>
|
||||
<orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
|
||||
<pruneDeadBranches>true</pruneDeadBranches>
|
||||
<daysToKeep>-1</daysToKeep>
|
||||
<numToKeep>-1</numToKeep>
|
||||
</orphanedItemStrategy>
|
||||
<triggers/>
|
||||
<disabled>false</disabled>
|
||||
<sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
|
||||
<data>
|
||||
<jenkins.branch.BranchSource>
|
||||
<source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
|
||||
<id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
|
||||
<remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tools.git</remote>
|
||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||
<traits>
|
||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
||||
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
|
||||
<localBranch>**</localBranch>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.LocalBranchTrait>
|
||||
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
|
||||
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
|
||||
<name>MOLGENIS Jenkins</name>
|
||||
<email>molgenis+ci@gmail.com</email>
|
||||
</extension>
|
||||
</jenkins.plugins.git.traits.UserIdentityTrait>
|
||||
</traits>
|
||||
</source>
|
||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||
<properties class="empty-list"/>
|
||||
</strategy>
|
||||
</jenkins.branch.BranchSource>
|
||||
</data>
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
</sources>
|
||||
<factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
|
||||
<owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
|
||||
<scriptPath>Jenkinsfile</scriptPath>
|
||||
</factory>
|
||||
</org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
|
||||
# Kubernetes secret that contains a 'credentials.xml' for Jenkins
|
||||
# CredentialsXmlSecret: jenkins-credentials
|
||||
# Kubernetes secret that contains files to be put in the Jenkins 'secrets' directory,
|
||||
# useful to manage encryption keys used for credentials.xml for instance (such as
|
||||
# master.key and hudson.util.Secret)
|
||||
# SecretsFilesSecret: jenkins-secrets
|
||||
CustomConfigMap: true
|
||||
rbac:
|
||||
install: true
|
||||
Pods:
|
||||
molgenis:
|
||||
Label: molgenis
|
||||
NodeUsageMode: NORMAL
|
||||
volumes:
|
||||
- type: HostPath
|
||||
hostPath: "/var/run/docker.sock"
|
||||
mountPath: "/var/run/docker.sock"
|
||||
Containers:
|
||||
maven:
|
||||
Image: "registry.webhosting.rug.nl/molgenis/maven"
|
||||
ImageTag: lts
|
||||
AlwaysPullImage: true
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
resources:
|
||||
requests:
|
||||
cpu: "1"
|
||||
memory: "4Gi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: MAVEN_OPTS
|
||||
value: "-Duser.home=/home/jenkins"
|
||||
- type: KeyValue
|
||||
key: MAVEN_CONFIG
|
||||
value: "/home/jenkins/.m2"
|
||||
alpine:
|
||||
Image: "spotify/alpine"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
vault:
|
||||
Image: "vault"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
EnvVars:
|
||||
- type: Secret
|
||||
key: VAULT_TOKEN
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: token
|
||||
- type: Secret
|
||||
key: VAULT_SKIP_VERIFY
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: skipVerify
|
||||
- type: Secret
|
||||
key: VAULT_ADDR
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: addr
|
||||
helm:
|
||||
Image: "lachlanevenson/k8s-helm"
|
||||
ImageTag: "v2.10.0"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
NodeSelector: {}
|
||||
node:
|
||||
Label: node-carbon
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
Containers:
|
||||
node:
|
||||
Image: "registry.webhosting.rug.nl/molgenis/node"
|
||||
ImageTag: lts
|
||||
AlwaysPullImage: true
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
vault:
|
||||
Image: "vault"
|
||||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
EnvVars:
|
||||
- type: Secret
|
||||
key: VAULT_TOKEN
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: token
|
||||
- type: Secret
|
||||
key: VAULT_SKIP_VERIFY
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: skipVerify
|
||||
- type: Secret
|
||||
key: VAULT_ADDR
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: addr
|
||||
NodeSelector: {}
|
||||
molgenis-it:
|
||||
InheritFrom: molgenis
|
||||
Label: molgenis-it
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
Containers:
|
||||
elasticsearch:
|
||||
Image: docker.elastic.co/elasticsearch/elasticsearch
|
||||
ImageTag: 5.5.3
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "1Gi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "1500Mi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: ES_JAVA_OPTS
|
||||
value: "-Xms512m -Xmx512m"
|
||||
- type: KeyValue
|
||||
key: cluster.name
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: bootstrap.memory_lock
|
||||
value: "true"
|
||||
- type: KeyValue
|
||||
key: xpack.security.enabled
|
||||
value: "false"
|
||||
- type: KeyValue
|
||||
key: discovery.type
|
||||
value: single-node
|
||||
postgres:
|
||||
Image: postgres
|
||||
ImageTag: 9.6-alpine
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "250Mi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "250Mi"
|
||||
EnvVars:
|
||||
- type: KeyValue
|
||||
key: POSTGRES_USER
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: POSTGRES_PASSWORD
|
||||
value: molgenis
|
||||
- type: KeyValue
|
||||
key: POSTGRES_DB
|
||||
value: molgenis
|
||||
opencpu:
|
||||
Image: molgenis/opencpu
|
||||
AlwaysPullImage: true
|
||||
resources:
|
||||
requests:
|
||||
cpu: "100m"
|
||||
memory: "256Mi"
|
||||
limits:
|
||||
cpu: "1"
|
||||
memory: "512Mi"
|
||||
NodeSelector: {}
|
||||
|
||||
# secret contains configuration for the kubernetes secrets that jenkins can access
|
||||
secret:
|
||||
# vault configures the vault secret
|
||||
vault:
|
||||
token: xxxx
|
||||
addr: "https://vault-operator.vault-operator.svc:8200"
|
||||
skipVerify: "1"
|
||||
# githubToken contains access token for jenkins bot account on github.com
|
||||
gitHub:
|
||||
user: "molgenis-jenkins"
|
||||
token: xxxx
|
||||
# gogs contains access token for jenkins bot account on RuG GoGs
|
||||
gogs:
|
||||
user: p281392
|
||||
token: xxxx
|
||||
# registry contains credentials for registry.molgenis.org
|
||||
registry:
|
||||
user: admin
|
||||
password: xxxx
|
||||
# dockerHubPassword contains password for hub.docker.com
|
||||
dockerHub:
|
||||
user: molgenisci
|
||||
password: xxxx
|
||||
|
|
@ -6,3 +6,7 @@ version: 0.4.2
|
|||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg
|
||||
home: https://www.sonatype.com/nexus-repository-oss
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
# 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.
|
||||
|
||||
|
||||
|
Before Width: | Height: | Size: 42 KiB After Width: | Height: | Size: 42 KiB |
|
|
@ -6,3 +6,7 @@ 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
|
||||
|
Before Width: | Height: | Size: 245 KiB After Width: | Height: | Size: 245 KiB |
|
|
@ -0,0 +1,35 @@
|
|||
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 }}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
# 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: {}
|
||||
|
|
@ -4,3 +4,7 @@ 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
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
# 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`
|
||||
|
Before Width: | Height: | Size: 46 KiB After Width: | Height: | Size: 46 KiB |
|
|
@ -0,0 +1,79 @@
|
|||
# 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
|
||||
|
|
@ -6,3 +6,7 @@ version: 0.4.3
|
|||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||
home: http://molgenis.org
|
||||
maintainers:
|
||||
- name: sidohaakma
|
||||
- name: fdlk
|
||||
|
Before Width: | Height: | Size: 77 KiB After Width: | Height: | Size: 77 KiB |
|
|
@ -0,0 +1,103 @@
|
|||
# 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: {}
|
||||
|
|
@ -1,6 +1,6 @@
|
|||
name: molgenis-jenkins
|
||||
home: https://jenkins.io/
|
||||
version: 0.7.1
|
||||
version: 0.8.0
|
||||
appVersion: 2.121
|
||||
description: Molgenis installation for the jenkins chart.
|
||||
sources:
|
||||
|
|
|
|||
|
|
@ -75,6 +75,10 @@ Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.w
|
|||
| `secret.gogs.user` | username for the account | `p281392` |
|
||||
| `secret.gogs.token` | token for the account | `xxxx` |
|
||||
|
||||
|
||||
#### Slack
|
||||
The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
|
||||
|
||||
#### Legacy:
|
||||
|
||||
##### Docker Hub
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
# 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
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
jenkins:
|
||||
Master:
|
||||
NodeSelector:
|
||||
deployPod: "true"
|
||||
HostName: jenkins.molgenis.org
|
||||
ServiceType: ClusterIP
|
||||
InstallPlugins:
|
||||
|
|
@ -14,6 +16,7 @@ jenkins:
|
|||
- github-oauth:0.29
|
||||
- gogs-webhook:1.0.14
|
||||
- github-scm-trait-commit-skip:0.1.1
|
||||
- slack:2.3
|
||||
Security:
|
||||
UseGitHub: false
|
||||
GitHub:
|
||||
|
|
@ -489,7 +492,9 @@ jenkins:
|
|||
Command: cat
|
||||
WorkingDir: /home/jenkins
|
||||
TTY: true
|
||||
NodeSelector: {}
|
||||
NodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
node:
|
||||
Label: node-carbon
|
||||
NodeUsageMode: EXCLUSIVE
|
||||
|
|
@ -519,7 +524,9 @@ jenkins:
|
|||
key: VAULT_ADDR
|
||||
secretName: molgenis-pipeline-vault-secret
|
||||
secretKey: addr
|
||||
NodeSelector: {}
|
||||
NodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
molgenis-it:
|
||||
InheritFrom: molgenis
|
||||
Label: molgenis-it
|
||||
|
|
@ -581,7 +588,9 @@ jenkins:
|
|||
limits:
|
||||
cpu: "1"
|
||||
memory: "512Mi"
|
||||
NodeSelector: {}
|
||||
NodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
|
||||
#secret contains configuration for the kubernetes secrets that jenkins can access
|
||||
secret:
|
||||
|
|
|
|||
|
|
@ -61,4 +61,9 @@ To test if your hem chart works and:
|
|||
|
||||
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
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -31,5 +31,7 @@ spec:
|
|||
ports:
|
||||
- containerPort: {{ .service.port }}
|
||||
{{- end }}
|
||||
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
|
|
|
|||
|
|
@ -34,7 +34,9 @@ ingress:
|
|||
- name: opencpu.molgenis.org
|
||||
tls: []
|
||||
|
||||
nodeSelector: {}
|
||||
nodeSelector: {
|
||||
deployPod: "true"
|
||||
}
|
||||
|
||||
tolerations: []
|
||||
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ Parameter | Description | Default
|
|||
`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.nodeSelector` | node labels for Vault UI pod assignment | `{deployPod: "true"}`
|
||||
`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`
|
||||
|
|
|
|||
|
|
@ -18,6 +18,10 @@ backupJob:
|
|||
# schedule gives the cron schedule for the backup job
|
||||
schedule: "0 12 * * 1"
|
||||
|
||||
vault-operator:
|
||||
nodeSelector:
|
||||
deployPod: "true"
|
||||
|
||||
###
|
||||
# All of the config variables related to setting up the etcd-operator
|
||||
# If you want more information about the variables exposed, please visit:
|
||||
|
|
@ -44,6 +48,8 @@ etcd-operator:
|
|||
restoreOperator:
|
||||
image:
|
||||
tag: v0.9.2
|
||||
nodeSelector:
|
||||
deployPod: "true"
|
||||
|
||||
ui:
|
||||
name: "vault-ui"
|
||||
|
|
@ -73,7 +79,8 @@ ui:
|
|||
#requests:
|
||||
# cpu: 100m
|
||||
# memory: 128Mi
|
||||
nodeSelector: {}
|
||||
nodeSelector:
|
||||
deployPod: "true"
|
||||
vault:
|
||||
auth: GITHUB
|
||||
url: https://vault.vault-operator:8200
|
||||
|
|
@ -94,9 +94,8 @@ persistence:
|
|||
enabled: true
|
||||
retain: false
|
||||
|
||||
nodeSelector: {
|
||||
nodeSelector:
|
||||
deployPod: "true"
|
||||
}
|
||||
|
||||
tolerations: []
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue