diff --git a/molgenis-httpd/v0.1.x/.helmignore b/molgenis-httpd/v0.1.x/.helmignore new file mode 100644 index 0000000..f0c1319 --- /dev/null +++ b/molgenis-httpd/v0.1.x/.helmignore @@ -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 diff --git a/molgenis-httpd/v0.1.x/Chart.yaml b/molgenis-httpd/v0.1.x/Chart.yaml new file mode 100644 index 0000000..b22d6fb Binary files /dev/null and b/molgenis-httpd/v0.1.x/Chart.yaml differ diff --git a/molgenis-httpd/v0.1.x/README.md b/molgenis-httpd/v0.1.x/README.md new file mode 100644 index 0000000..6f7a8df --- /dev/null +++ b/molgenis-httpd/v0.1.x/README.md @@ -0,0 +1,15 @@ +# MOLGENIS - HTTPD Helm Chart + +HTTPD (web)server for kubernetes to deploy on a kubernetes cluster with NFS-share + +## Chart Details + +This chart will deploy: + +- 1 HTTPD container + +## Installing the Chart + +etc. + + diff --git a/molgenis-httpd/v0.1.x/questions.yml b/molgenis-httpd/v0.1.x/questions.yml new file mode 100644 index 0000000..623c3cf --- /dev/null +++ b/molgenis-httpd/v0.1.x/questions.yml @@ -0,0 +1,31 @@ +categories: +- MOLGENIS +questions: +- variable: ingress.hosts[0].name + default: "test.molgenis.org" + description: "Hostname for your stack" + type: hostname + required: true + group: "Services and Load Balancing" + label: Hostname +- variable: httpd.hostname + default: "test.molgenis.org" + description: "Hostname for your services (comma separated, example: [hostname]:[port])" + type: string + required: false + group: "Apache configuration" + label: Hostname +- variable: httpd.proxy + default: "" + description: "Proxy for your services (comma separated, example: [service]:[port]:[path])" + type: string + required: false + group: "Apache configuration" + label: Proxy +- variable: httpd.redirect + default: "" + description: "Redirection urls for your services (comma separated, example: [redirection_url])" + type: string + required: false + group: "Apache configuration" + label: Redirection \ No newline at end of file diff --git a/molgenis-httpd/v0.1.x/templates/NOTES.txt b/molgenis-httpd/v0.1.x/templates/NOTES.txt new file mode 100644 index 0000000..b486fa5 --- /dev/null +++ b/molgenis-httpd/v0.1.x/templates/NOTES.txt @@ -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 "httpd.fullname" . }}) + export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}") + echo http://$NODE_IP:$NODE_PORT +{{- else if contains "LoadBalancer" .Values.service.type }} + NOTE: It may take a few minutes for the LoadBalancer IP to be available. + You can watch the status of by running 'kubectl get svc -w {{ template "httpd.fullname" . }}' + export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "httpd.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 "httpd.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 }} diff --git a/molgenis-httpd/v0.1.x/templates/_helpers.tpl b/molgenis-httpd/v0.1.x/templates/_helpers.tpl new file mode 100644 index 0000000..6968597 --- /dev/null +++ b/molgenis-httpd/v0.1.x/templates/_helpers.tpl @@ -0,0 +1,32 @@ +{{/* vim: set filetype=mustache: */}} +{{/* +Expand the name of the chart. +*/}} +{{- define "httpd.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 "httpd.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 "httpd.chart" -}} +{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} +{{- end -}} diff --git a/molgenis-httpd/v0.1.x/templates/deployment.yaml b/molgenis-httpd/v0.1.x/templates/deployment.yaml new file mode 100644 index 0000000..a55964a --- /dev/null +++ b/molgenis-httpd/v0.1.x/templates/deployment.yaml @@ -0,0 +1,57 @@ +apiVersion: apps/v1beta2 +kind: Deployment +metadata: + name: {{ template "httpd.fullname" . }} + labels: + app: {{ template "httpd.name" . }} + chart: {{ template "httpd.chart" . }} + release: {{ .Release.Name }} + heritage: {{ .Release.Service }} +spec: + replicas: {{ .Values.replicaCount }} + selector: + matchLabels: + app: {{ template "httpd.name" . }} + release: {{ .Release.Name }} + template: + metadata: + labels: + app: {{ template "httpd.name" . }} + release: {{ .Release.Name }} + spec: + containers: + - name: {{ .Chart.Name }} + image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}" + imagePullPolicy: {{ .Values.image.pullPolicy }} + ports: + - name: {{ .Values.service.name }} + containerPort: {{ .Values.service.port }} + env: + - name: SERVER_NAME + value: "{{ .Values.httpd.hostname }}" + - name: PROXY_SERVICE + value: "{{ .Values.httpd.proxy }}" + - name: REDIRECT_URL + value: "{{ .Values.httpd.redirect }}" + livenessProbe: + httpGet: + path: / + port: http + readinessProbe: + httpGet: + path: / + port: http + resources: +{{ toYaml .Values.resources | indent 12 }} + {{- with .Values.nodeSelector }} + nodeSelector: +{{ toYaml . | indent 8 }} + {{- end }} + {{- with .Values.affinity }} + affinity: +{{ toYaml . | indent 8 }} + {{- end }} + {{- with .Values.tolerations }} + tolerations: +{{ toYaml . | indent 8 }} + {{- end }} diff --git a/molgenis-httpd/v0.1.x/templates/ingress.yaml b/molgenis-httpd/v0.1.x/templates/ingress.yaml new file mode 100644 index 0000000..83a8d70 --- /dev/null +++ b/molgenis-httpd/v0.1.x/templates/ingress.yaml @@ -0,0 +1,36 @@ +{{- if .Values.ingress.enabled }} +{{- range .Values.ingress.hosts }} +apiVersion: extensions/v1beta1 +kind: Ingress +metadata: + name: "{{ $.Release.Name }}-ingress" + labels: + app: {{ template "httpd.fullname" $ }} + chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}" + release: "{{ $.Release.Name }}" + heritage: "{{ $.Release.Service }}" + annotations: + {{- if .tls }} + ingress.kubernetes.io/secure-backends: "true" + {{- end }} + {{- range $key, $value := .annotations }} + {{ $key }}: {{ $value | quote }} + {{- end }} +spec: + rules: + - host: {{ .name }} + http: + paths: + - path: {{ default "/" .path }} + backend: + serviceName: {{ template "httpd.fullname" $ }} + servicePort: 80 +{{- if .tls }} + tls: + - hosts: + - {{ .name }} + secretName: {{ .tlsSecret }} +{{- end }} +--- +{{- end }} +{{- end }} \ No newline at end of file diff --git a/molgenis-httpd/v0.1.x/templates/service.yaml b/molgenis-httpd/v0.1.x/templates/service.yaml new file mode 100644 index 0000000..b3f1374 --- /dev/null +++ b/molgenis-httpd/v0.1.x/templates/service.yaml @@ -0,0 +1,18 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ template "httpd.fullname" . }} + labels: + app: {{ template "httpd.name" . }} + chart: {{ template "httpd.chart" . }} + release: {{ .Release.Name }} + heritage: {{ .Release.Service }} +spec: + type: {{ .Values.service.type }} + ports: + - name: {{ .Values.service.name }} + port: {{ .Values.service.port }} + + selector: + app: {{ template "httpd.name" . }} + release: {{ .Release.Name }} diff --git a/molgenis-httpd/v0.1.x/values.yaml b/molgenis-httpd/v0.1.x/values.yaml new file mode 100644 index 0000000..04fffb6 --- /dev/null +++ b/molgenis-httpd/v0.1.x/values.yaml @@ -0,0 +1,51 @@ +# Default values for jenkins. +# This is a YAML-formatted file. +# Declare variables to be passed into your templates. + +replicaCount: 1 + +image: + repository: registry.webhosting.rug.nl/molgenis/httpd + tag: lts + pullPolicy: Always + +service: + name: httpd + type: ClusterIP + port: 80 + +httpd: + proxy: httpd:80:/ + redirect: redirect.molgenis.local + hostname: test.molgenis.local + +ingress: + enabled: true + annotations: {} + # kubernetes.io/ingress.class: nginx + # kubernetes.io/tls-acme: "true" + path: / + hosts: + - name: test.molgenis.org + tls: [] + # - secretName: chart-example-tls + # hosts: + # - chart-example.local + +resources: {} + # We usually recommend not to specify default resources and to leave this as a conscious + # choice for the user. This also increases chances charts run on environments with little + # resources, such as Minikube. If you do want to specify resources, uncomment the following + # lines, adjust them as necessary, and remove the curly braces after 'resources:'. + # limits: + # cpu: 100m + # memory: 128Mi + # requests: + # cpu: 100m + # memory: 128Mi + +nodeSelector: {} + +tolerations: [] + +affinity: {} \ No newline at end of file diff --git a/molgenis-nexus/README.md b/molgenis-nexus/README.md new file mode 100644 index 0000000..b9a3b21 --- /dev/null +++ b/molgenis-nexus/README.md @@ -0,0 +1,16 @@ +# MOLGENIS - NEXUS Helm Chart + +NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share + +## Chart Details + +This chart will deploy: + +- 1 NEXUS container +- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain) + +## Installing the Chart + +etc. + + diff --git a/molgenis-nexus/v0.2.x/.helmignore b/molgenis-nexus/v0.2.x/.helmignore new file mode 100644 index 0000000..f0c1319 --- /dev/null +++ b/molgenis-nexus/v0.2.x/.helmignore @@ -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 diff --git a/molgenis-nexus/v0.2.x/Chart.yaml b/molgenis-nexus/v0.2.x/Chart.yaml new file mode 100644 index 0000000..575a62a --- /dev/null +++ b/molgenis-nexus/v0.2.x/Chart.yaml @@ -0,0 +1,6 @@ +apiVersion: v1 +appVersion: "1.0" +description: Nexus stack for MOLGENIS +name: molgenis-nexus +version: 0.2.0 +icon: https://github.com/sidohaakma/molgenis-docker-helm/blob/master/nexus/catalogIcon-molgenis-nexus.svg \ No newline at end of file diff --git a/molgenis-nexus/v0.2.x/catalogIcon-molgenis-nexus.svg b/molgenis-nexus/v0.2.x/catalogIcon-molgenis-nexus.svg new file mode 100644 index 0000000..9c7d611 --- /dev/null +++ b/molgenis-nexus/v0.2.x/catalogIcon-molgenis-nexus.svg @@ -0,0 +1,551 @@ + + + + diff --git a/molgenis-nexus/v0.2.x/templates/_helpers.tpl b/molgenis-nexus/v0.2.x/templates/_helpers.tpl new file mode 100644 index 0000000..9f9800c --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/_helpers.tpl @@ -0,0 +1,32 @@ +{{/* vim: set filetype=mustache: */}} +{{/* +Expand the name of the chart. +*/}} +{{- define "nexus.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 "nexus.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 "nexus.chart" -}} +{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} +{{- end -}} diff --git a/molgenis-nexus/v0.2.x/templates/deployments/httpd-deployment.yaml b/molgenis-nexus/v0.2.x/templates/deployments/httpd-deployment.yaml new file mode 100644 index 0000000..cbf1c0f --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/deployments/httpd-deployment.yaml @@ -0,0 +1,34 @@ +apiVersion: extensions/v1beta1 +kind: Deployment +metadata: + creationTimestamp: null + name: {{ .Values.httpd.name }} + labels: + app: {{ .Values.httpd.name }} + environment: {{ .Values.environment }} +spec: + replicas: {{ .Values.replicaCount }} + strategy: + type: {{ .Values.httpd.strategy.type }} + selector: + matchLabels: + app: {{ .Values.httpd.selector }} + template: + metadata: + labels: + app: {{ .Values.httpd.name }} + creationTimestamp: null + spec: + restartPolicy: {{ .Values.httpd.restartPolicy }} + containers: + - name: {{ .Values.httpd.name }} + image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}" + imagePullPolicy: {{ .Values.httpd.image.pullPolicy }} + env: + - name: PROXY_SERVICE + value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}" + - name: SERVER_NAME + value: {{ .Values.httpd.hostname }} + ports: + - containerPort: {{ .Values.httpd.port }} + resources: {} \ No newline at end of file diff --git a/molgenis-nexus/v0.2.x/templates/deployments/nexus-deployment.yaml b/molgenis-nexus/v0.2.x/templates/deployments/nexus-deployment.yaml new file mode 100644 index 0000000..96d04f4 --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/deployments/nexus-deployment.yaml @@ -0,0 +1,44 @@ +apiVersion: extensions/v1beta1 +kind: Deployment +metadata: + creationTimestamp: null + name: {{ .Values.nexus.name }} + labels: + app: {{ .Values.nexus.name }} + environment: {{ .Values.environment }} +spec: + replicas: {{ .Values.replicaCount }} + strategy: + type: {{ .Values.nexus.strategy.type }} + selector: + matchLabels: + app: {{ .Values.nexus.selector }} + template: + metadata: + labels: + app: {{ .Values.nexus.name }} + creationTimestamp: null + spec: + volumes: + - name: {{ .Values.persistence.name }} + persistentVolumeClaim: + claimName: {{ .Values.persistence.name }} + restartPolicy: {{ .Values.nexus.restartPolicy }} + initContainers: + - name: volume-mount-nexus + image: busybox + command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"] + volumeMounts: + - name: {{ .Values.persistence.name }} + mountPath: "{{ .Values.persistence.mountPath }}" + containers: + - name: {{ .Values.nexus.name }} + image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}" + imagePullPolicy: {{ .Values.nexus.image.pullPolicy }} + ports: + - containerPort: {{ .Values.nexus.port.ui }} + - containerPort: {{ .Values.nexus.port.docker }} + volumeMounts: + - name: {{ .Values.persistence.name }} + mountPath: "/nexus-data" + diff --git a/molgenis-nexus/v0.2.x/templates/ingress.yaml b/molgenis-nexus/v0.2.x/templates/ingress.yaml new file mode 100644 index 0000000..9df4d02 --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/ingress.yaml @@ -0,0 +1,38 @@ +{{- if .Values.ingress.enabled }} +{{- range .Values.ingress.hosts }} +apiVersion: extensions/v1beta1 +kind: Ingress +metadata: + name: "{{ $.Release.Name }}-ingress" + labels: + app: httpd + chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}" + release: "{{ $.Release.Name }}" + heritage: "{{ $.Release.Service }}" + annotations: + kubernetes.io/ingress.class: "nginx" + nginx.ingress.kubernetes.io/proxy-body-size: "0" + {{- if .tls }} + ingress.kubernetes.io/secure-backends: "true" + {{- end }} + {{- range $key, $value := .annotations }} + {{ $key }}: {{ $value | quote }} + {{- end }} +spec: + rules: + - host: {{ .name }} + http: + paths: + - path: {{ default "/" .path }} + backend: + serviceName: httpd + servicePort: 80 +{{- if .tls }} + tls: + - hosts: + - {{ .name }} + secretName: {{ .tlsSecret }} +{{- end }} +--- +{{- end }} +{{- end }} \ No newline at end of file diff --git a/molgenis-nexus/v0.2.x/templates/services/nexus-service.yaml b/molgenis-nexus/v0.2.x/templates/services/nexus-service.yaml new file mode 100644 index 0000000..bc0fda7 --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/services/nexus-service.yaml @@ -0,0 +1,15 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ .Values.nexus.name }} + labels: + app: {{ .Values.nexus.name }} +spec: + type: ClusterIP + ports: + - name: ui + port: {{ .Values.nexus.port.ui }} + - name: docker + port: {{ .Values.nexus.port.docker }} + selector: + app: {{ .Values.nexus.selector }} diff --git a/molgenis-nexus/v0.2.x/templates/volumes/nexus-pv.yaml b/molgenis-nexus/v0.2.x/templates/volumes/nexus-pv.yaml new file mode 100644 index 0000000..95c6f71 --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/volumes/nexus-pv.yaml @@ -0,0 +1,16 @@ +apiVersion: v1 +kind: PersistentVolume +metadata: + name: {{ .Values.persistence.name }} + labels: + name: nfs2 +spec: + storageClassName: {{ .Values.persistence.storageClass }} + capacity: + storage: {{ .Values.persistence.size }} + accessModes: + - {{ .Values.persistence.accessMode }} + persistentVolumeReclaimPolicy: {{ .Values.persistence.reclaimPolicy }} + nfs: + server: {{ .Values.persistence.server }} + path: {{ .Values.persistence.mountPath }} diff --git a/molgenis-nexus/v0.2.x/templates/volumes/nexus-pvc.yaml b/molgenis-nexus/v0.2.x/templates/volumes/nexus-pvc.yaml new file mode 100644 index 0000000..3b2d4bb --- /dev/null +++ b/molgenis-nexus/v0.2.x/templates/volumes/nexus-pvc.yaml @@ -0,0 +1,11 @@ +kind: PersistentVolumeClaim +apiVersion: v1 +metadata: + name: {{ .Values.persistence.name }} +spec: + storageClassName: {{ .Values.persistence.storageClass }} + accessModes: + - {{ .Values.persistence.accessMode }} + resources: + requests: + storage: {{ .Values.persistence.size }} \ No newline at end of file diff --git a/molgenis-nexus/v0.2.x/values.yaml b/molgenis-nexus/v0.2.x/values.yaml new file mode 100644 index 0000000..32c193c --- /dev/null +++ b/molgenis-nexus/v0.2.x/values.yaml @@ -0,0 +1,82 @@ +# Default values for nexus. +# This is a YAML-formatted file. +# Declare variables to be passed into your templates. + +replicaCount: 1 + +environment: production + +service: + type: NodePort + port: 80 + +nexus: + name: nexus + strategy: + type: Recreate + selector: nexus + restartPolicy: Always + image: + repository: sonatype/nexus3 + tag: latest + pullPolicy: Always + port: + docker: 5000 + ui: 8081 + path: + dockerV2: v2 + +httpd: + name: httpd + hostname: registry.molgenis.org + strategy: + type: Recreate + selector: httpd + restartPolicy: Always + image: + repository: registry.webhosting.rug.nl/molgenis/httpd + tag: lts + pullPolicy: Always + port: 80 + + +ingress: + enabled: true + annotations: {} + # kubernetes.io/ingress.class: nginx + # kubernetes.io/tls-acme: "true" + path: / + hosts: + - name: registry.molgenis.org + tls: [] + # - secretName: chart-example-tls + # hosts: + # - chart-example.local + +persistence: + name: molgenis-nexus-data + storageClass: nfs-class + size: 30G + reclaimPolicy: Retain + server: 192.168.64.12 + accessMode: ReadWriteMany + mountPath: /gcc/molgenis/nexus + + +resources: {} + # We usually recommend not to specify default resources and to leave this as a conscious + # choice for the user. This also increases chances charts run on environments with little + # resources, such as Minikube. If you do want to specify resources, uncomment the following + # lines, adjust them as necessary, and remove the curly braces after 'resources:'. + # limits: + # cpu: 100m + # memory: 128Mi + # requests: + # cpu: 100m + # memory: 128Mi + +nodeSelector: {} + +tolerations: [] + +affinity: {}