molgenis-ops-docker-helm/molgenis-jenkins/README.md

Molgenis Jenkins Helm Chart

Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin

• https://wiki.jenkins-ci.org/display/JENKINS/Kubernetes+Plugin

Inspired by the awesome work of Carlos Sanchez mailto:carlos@apache.org

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

In the rancher UI, choose the molgenis-jenkins app from the catalog and deploy it.

Configuration

The following tables list the configurable parameters of the Jenkins chart and their default values. You can paste these values into the Rancher Answers if you like. Array values can be added as {value, value, value}, e.g.

jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1}

Because we use jenkins as a sub-chart, you should prefix all values with jenkins!

Jenkins Master

Parameter	Description	Default
nameOverride	Override the resource name prefix	jenkins
fullnameOverride	Override the full resource names	jenkins-{release-name} (or jenkins if release-name is jenkins)
Master.Name	Jenkins master name	jenkins-master
Master.Image	Master image name	jenkinsci/jenkins
Master.ImageTag	Master image tag	lts
Master.ImagePullPolicy	Master image pull policy	Always
Master.ImagePullSecret	Master image pull secret	Not set
Master.Component	k8s selector key	jenkins-master
Master.UseSecurity	Use basic security	true
Master.AdminUser	Admin username (and password) created as a secret if useSecurity is true	admin
Master.Cpu	Master requested cpu	200m
Master.Memory	Master requested memory	256Mi
Master.InitContainerEnv	Environment variables for Init Container	Not set
Master.ContainerEnv	Environment variables for Jenkins Container	Not set
Master.RunAsUser	uid that jenkins runs with	0
Master.FsGroup	uid that will be used for persistent volume	0
Master.ServiceAnnotations	Service annotations	{}
Master.ServiceType	k8s service type	LoadBalancer
Master.ServicePort	k8s service port	8080
Master.NodePort	k8s node port	Not set
Master.HealthProbes	Enable k8s liveness and readiness probes	true
Master.HealthProbesLivenessTimeout	Set the timeout for the liveness probe	120
Master.HealthProbesReadinessTimeout	Set the timeout for the readiness probe	60
Master.HealthProbeLivenessFailureThreshold	Set the failure threshold for the liveness probe	12
Master.ContainerPort	Master listening port	8080
Master.SlaveListenerPort	Listening port for agents	50000
Master.DisabledAgentProtocols	Disabled agent protocols	JNLP-connect JNLP2-connect
Master.CSRF.DefaultCrumbIssuer.Enabled	Enable the default CSRF Crumb issuer	true
Master.CSRF.DefaultCrumbIssuer.ProxyCompatability	Enable proxy compatibility	true
Master.CLI	Enable CLI over remoting	false
Master.LoadBalancerSourceRanges	Allowed inbound IP addresses	0.0.0.0/0
Master.LoadBalancerIP	Optional fixed external IP	Not set
Master.JMXPort	Open a port, for JMX stats	Not set
Master.CustomConfigMap	Use a custom ConfigMap	false
Master.Ingress.Annotations	Ingress annotations	{}
Master.Ingress.TLS	Ingress TLS configuration	[]
Master.InitScripts	List of Jenkins init scripts	Not set
Master.CredentialsXmlSecret	Kubernetes secret that contains a 'credentials.xml' file	Not set
Master.SecretsFilesSecret	Kubernetes secret that contains 'secrets' files	Not set
Master.Jobs	Jenkins XML job configs	Not set
Master.InstallPlugins	List of Jenkins plugins to install	kubernetes:0.11 workflow-aggregator:2.5 credentials-binding:1.11 git:3.2.0
Master.ScriptApproval	List of groovy functions to approve	Not set
Master.NodeSelector	Node labels for pod assignment	{}
Master.Affinity	Affinity settings	{}
Master.Tolerations	Toleration labels for pod assignment	{}
NetworkPolicy.Enabled	Enable creation of NetworkPolicy resources.	false
NetworkPolicy.ApiVersion	NetworkPolicy ApiVersion	extensions/v1beta1
rbac.install	Create service account and ClusterRoleBinding for Kubernetes plugin	false
rbac.apiVersion	RBAC API version	v1beta1
rbac.roleRef	Cluster role name to bind to	cluster-admin

Jenkins Agent

Parameter	Description	Default
Agent.AlwaysPullImage	Always pull agent container image before build	false
Agent.Enabled	Enable Kubernetes plugin jnlp-agent podTemplate	true
Agent.Image	Agent image name	jenkinsci/jnlp-slave
Agent.ImagePullSecret	Agent image pull secret	Not set
Agent.ImageTag	Agent image tag	2.62
Agent.Privileged	Agent privileged container	false
Agent.Cpu	Agent requested cpu	200m
Agent.Memory	Agent requested memory	256Mi
Agent.volumes	Additional volumes	nil

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,

$ helm install --name my-release -f values.yaml stable/jenkins

Tip: You can use the default values.yaml

Mounting volumes into your Agent pods

Your Jenkins Agents will run as pods, and it's possible to inject volumes where needed:

Agent:
  volumes:
  - type: Secret
    secretName: jenkins-mysecrets
    mountPath: /var/run/secrets/jenkins-mysecrets

The supported volume types are: ConfigMap, EmptyDir, HostPath, Nfs, Pod, Secret. Each type supports a different set of configurable attributes, defined by the corresponding Java class.

NetworkPolicy

To make use of the NetworkPolicy resources created by default, install a networking plugin that implements the Kubernetes NetworkPolicy spec.

For Kubernetes v1.5 & v1.6, you must also turn on NetworkPolicy by setting the DefaultDeny namespace annotation. Note: this will enforce policy for all pods in the namespace:

kubectl annotate namespace default "net.beta.kubernetes.io/network-policy={\"ingress\":{\"isolation\":\"DefaultDeny\"}}"

Install helm chart with network policy enabled:

$ helm install stable/jenkins --set NetworkPolicy.Enabled=true

Persistence

The Jenkins image stores persistence under /var/jenkins_home path of the container. A dynamically managed Persistent Volume Claim is used to keep the data across deployments, by default. This is known to work in GCE, AWS, and minikube. Alternatively, a previously configured Persistent Volume Claim can be used.

It is possible to mount several volumes using Persistence.volumes and Persistence.mounts parameters.

Persistence Values

Parameter	Description	Default
Persistence.Enabled	Enable the use of a Jenkins PVC	true
Persistence.ExistingClaim	Provide the name of a PVC	nil
Persistence.AccessMode	The PVC access mode	ReadWriteOnce
Persistence.Size	The size of the PVC	8Gi
Persistence.volumes	Additional volumes	nil
Persistence.mounts	Additional mounts	nil

Existing PersistentVolumeClaim

1. Create the PersistentVolume
2. Create the PersistentVolumeClaim
3. Install the chart

$ helm install --name my-release --set Persistence.ExistingClaim=PVC_NAME stable/jenkins

Custom ConfigMap

When creating a new parent chart with this chart as a dependency, the CustomConfigMap parameter can be used to override the default config.xml provided. It also allows for providing additional xml configuration files that will be copied into /var/jenkins_home. In the parent chart's values.yaml, set the jenkins.Master.CustomConfigMap value to true like so

jenkins:
  Master:
    CustomConfigMap: true

and provide the file templates/config.tpl in your parent chart for your use case. You can start by copying the contents of config.yaml from this chart into your parent charts templates/config.tpl as a basis for customization. Finally, you'll need to wrap the contents of templates/config.tpl like so:

{{- define "override_config_map" }}
    <CONTENTS_HERE>
{{ end }}

RBAC

If running upon a cluster with RBAC enabled you will need to do the following:

• helm install stable/jenkins --set rbac.install=true
• Create a Jenkins credential of type Kubernetes service account with service account name provided in the helm status output.
• Under configure Jenkins -- Update the credentials config in the cloud section to use the service account credential you created in the step above.

Run Jenkins as non root user

The default settings of this helm chart let Jenkins run as root user with uid 0. Due to security reasons you may want to run Jenkins as a non root user. Fortunately the default jenkins docker image jenkins/jenkins contains a user jenkins with uid 1000 that can be used for this purpose.

Simply use the following settings to run Jenkins as jenkins user with uid 1000.

jenkins:
  Master:
    RunAsUser: 1000
    FsGroup: 1000

Docs taken from https://github.com/jenkinsci/docker/blob/master/Dockerfile: Jenkins is run with user jenkins, uid = 1000. If you bind mount a volume from the host or a data container,ensure you use the same uid

Running behind a forward proxy

The master pod uses an Init Container to install plugins etc. If you are behind a corporate proxy it may be useful to set Master.InitContainerEnv to add environment variables such as http_proxy, so that these can be downloaded.

Additionally, you may want to add env vars for the Jenkins container, and the JVM (Master.JavaOpts).

Master:
  InitContainerEnv:
    - name: http_proxy
      value: "http://192.168.64.1:3128"
    - name: https_proxy
      value: "http://192.168.64.1:3128"
    - name: no_proxy
      value: ""
  ContainerEnv:
    - name: http_proxy
      value: "http://192.168.64.1:3128"
    - name: https_proxy
      value: "http://192.168.64.1:3128"
  JavaOpts: >-
    -Dhttp.proxyHost=192.168.64.1
    -Dhttp.proxyPort=3128
    -Dhttps.proxyHost=192.168.64.1
    -Dhttps.proxyPort=3128