README.md

@@ -1,14 +1,8 @@
 # MOLGENIS Helm templates
 
-These are the Helm templates that we will use for MOLGENIS operations. There are some prerequisites you need.
 
-- docker
-- minikube
- 
 ## Useful commands for Kubernetes
 
-Commands that can be used to get information from a kubernetes cluster
-
 - kubectl get pods
   Gets alls running instances of containers from a certain deployment
 - kubectl get services
@@ -20,14 +14,6 @@ Commands that can be used to get information from a kubernetes cluster
 - kubectl get deployments
   Gets all deployments (comparable with docker-compose)
 
-When you want to see what is running on the clusters at the CIT you have to make a context switch.
-You can access the cluster with kubeconfig-files. You can obtain these by downloading them from the 
-MOLGENIS kubernetes cluster.
-
-- Goto https://rancher.molgenis.org:7443
-- Goto 
-
-
 ## Useful commands for Helm
 
 - helm install .

molgenis-jenkins/templates/config.tpl

@@ -91,67 +91,60 @@ data:
 {{- end }}
               <nodeProperties/>
             </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-{{- end -}}
-{{- if .Values.Pod.Enabled }}
             <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
               <inheritFrom></inheritFrom>
-              <name>{{ .Values.Pod.Label }}</name>
+              <name></name>
+              <namespace></namespace>
+              <privileged>false</privileged>
+              <capOnlyOnAlivePods>false</capOnlyOnAlivePods>
+              <alwaysPullImage>false</alwaysPullImage>
               <instanceCap>2147483647</instanceCap>
+              <slaveConnectTimeout>100</slaveConnectTimeout>
               <idleMinutes>0</idleMinutes>
-              <label>{{ .Values.Pod.Label }}</label>
+              <activeDeadlineSeconds>0</activeDeadlineSeconds>
-              <nodeSelector>
+              <label>molgenis-maven</label>
-                {{- $local := dict "first" true }}
+              <nodeSelector></nodeSelector>
-                {{- range $key, $value := .Values.Pod.NodeSelector }}
+              <nodeUsageMode>EXCLUSIVE</nodeUsageMode>
-                  {{- if not $local.first }},{{- end }}
+              <customWorkspaceVolumeEnabled>false</customWorkspaceVolumeEnabled>
-                  {{- $key }}={{ $value }}
+              <workspaceVolume class="org.csanchez.jenkins.plugins.kubernetes.volumes.workspace.EmptyDirWorkspaceVolume">
-                  {{- $_ := set $local "first" false }}
+                <memory>false</memory>
-                {{- end }}</nodeSelector>
+              </workspaceVolume>
-                <nodeUsageMode>NORMAL</nodeUsageMode>
               <volumes>
-{{- range $index, $volume := .Values.Pod.volumes }}
+                <org.csanchez.jenkins.plugins.kubernetes.volumes.HostPathVolume>
-                <org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
+                  <mountPath>/var/run/docker.sock</mountPath>
-{{- range $key, $value := $volume }}{{- if not (eq $key "type") }}
+                  <hostPath>/var/run/docker.sock</hostPath>
-                  <{{ $key }}>{{ $value }}</{{ $key }}>
+                </org.csanchez.jenkins.plugins.kubernetes.volumes.HostPathVolume>
-{{- end }}{{- end }}
-                </org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
-{{- end }}
               </volumes>
               <containers>
                 <org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
-                  <name>{{ .Values.Pod.Label }}</name>
+                  <name>maven</name>
-                  <image>{{ .Values.Pod.Image }}:{{ .Values.Pod.ImageTag }}</image>
+                  <image>webhost12.service.rug.nl/molgenis/molgenis-maven:latest</image>
-{{- if .Values.Pod.Privileged }}
-                  <privileged>true</privileged>
-{{- else }}
                   <privileged>false</privileged>
-{{- end }}
+                  <alwaysPullImage>true</alwaysPullImage>
-                  <alwaysPullImage>{{ .Values.Pod.AlwaysPullImage }}</alwaysPullImage>
                   <workingDir>/home/jenkins</workingDir>
-                  <command>{{ .Values.Pod.Command }}</command>
+                  <command>/bin/sh -c</command>
-                  <args>{{ .Values.Pod.Args }}</args>
+                  <args>cat</args>
-{{- if .Values.Pod.TTY }}
                   <ttyEnabled>true</ttyEnabled>
-{{- else }}
+                  <resourceRequestCpu></resourceRequestCpu>
-                  <ttyEnabled>false</ttyEnabled>
+                  <resourceRequestMemory></resourceRequestMemory>
-{{- end }}
+                  <resourceLimitCpu></resourceLimitCpu>
-                  <resourceRequestCpu>{{.Values.Pod.Cpu}}</resourceRequestCpu>
+                  <resourceLimitMemory></resourceLimitMemory>
-                  <resourceRequestMemory>{{.Values.Pod.Memory}}</resourceRequestMemory>
+                  <envVars/>
-                  <resourceLimitCpu>{{.Values.Pod.Cpu}}</resourceLimitCpu>
+                  <ports/>
-                  <resourceLimitMemory>{{.Values.Pod.Memory}}</resourceLimitMemory>
+                  <livenessProbe>
+                    <execArgs></execArgs>
+                    <timeoutSeconds>0</timeoutSeconds>
+                    <initialDelaySeconds>0</initialDelaySeconds>
+                    <failureThreshold>0</failureThreshold>
+                    <periodSeconds>0</periodSeconds>
+                    <successThreshold>0</successThreshold>
+                  </livenessProbe>
                 </org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
               </containers>
               <envVars/>
               <annotations/>
-{{- if .Values.Pod.ImagePullSecret }}
-              <imagePullSecrets>
-                <org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
-                  <name>{{ .Values.Pod.ImagePullSecret }}</name>
-                </org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
-              </imagePullSecrets>
-{{- else }}
               <imagePullSecrets/>
-{{- end }}
+              <yaml></yaml>
-              <nodeProperties/>
             </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
 {{- end -}}
           </templates>

molgenis-jenkins/values.yaml

@@ -69,33 +69,4 @@ jenkins:
     # SecretsFilesSecret: jenkins-secrets
     CustomConfigMap: true
   rbac:
-    install: true
+    install: true
-  # A second agent to configure a second pod template
-  Pod:
-    Enabled: true
-    Image: "webhost12.service.rug.nl/molgenis/molgenis-maven"
-    ImageTag: latest
-  # ImagePullSecret: jenkins
-    Label: "molgenis-maven"
-    Privileged: false
-    Cpu: "200m"
-    Memory: "256Mi"
-    # You may want to change this to true while testing a new image
-    AlwaysPullImage: true
-    Command: "/bin/sh -c"
-    Args: "cat"
-    TTY: true
-    # You can define the volumes that you want to mount for this container
-    # Allowed types are: ConfigMap, EmptyDir, HostPath, Nfs, Pod, Secret
-    # Configure the attributes as they appear in the corresponding Java class for that type
-    # https://github.com/jenkinsci/kubernetes-plugin/tree/master/src/main/java/org/csanchez/jenkins/plugins/kubernetes/volumes
-    volumes:
-      - type: "HostPath"
-        mountPath: "/var/run/docker.sock"
-        hostPath: "/var/run/docker.sock"
-    # - type: Secret
-    #   secretName: mysecret
-    #   mountPath: /var/myapp/mysecret
-    NodeSelector: {}
-    # Key Value selectors. Ex:
-    # jenkins-agent: v1

nexus/v0.1.x/templates/deployments/nexus-deployment.yaml

@@ -24,13 +24,6 @@ spec:
         persistentVolumeClaim:
           claimName: molgenis-nexus-data
       restartPolicy: {{ .Values.nexus.restartPolicy }}
-      initContainers:
-      - name: volume-mount-nexus
-        image: busybox
-        command: ["sh", "-c", "chown -R 200:200 /gcc/molgenis/nexus"]
-        volumeMounts:
-        - name: molgenis-nexus-data
-          mountPath: "/nexus-data"
       containers:
       - name: {{ .Values.nexus.name }}
         image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"

nexus/v0.1.x/templates/volumes/nexus-pv.yaml

@@ -13,4 +13,4 @@ spec:
   persistentVolumeReclaimPolicy: Retain
   nfs:
     server: 192.168.64.12
-    path: /gcc/molgenis/nexus
+    path: /gcc/molgenis/nexus-data