Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm

charts/index.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+entries:
+  molgenis-preview:
+  - apiVersion: v1
+    appVersion: "1.0"
+    created: 2018-09-11T16:11:49.165533266+02:00
+    description: MOLGENIS - helm stack for testing purposes
+    digest: e1174bd0d8a71bf4d23f5463521cf4dbcac39dc93f16cd842c92cda1a963f6b2
+    icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
+    name: molgenis-preview
+    sources:
+    - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
+    urls:
+    - molgenis-preview-0.2.0.tgz
+    version: 0.2.0
+generated: 2018-09-11T16:11:49.158086031+02:00

molgenis-jenkins/resources/README.md

@@ -1,6 +0,0 @@
-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

molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml

@@ -1,13 +0,0 @@
-apiVersion: rbac.authorization.k8s.io/v1beta1
-kind: RoleBinding
-metadata:
-  name: tiller-jenkins-binding
-  namespace: kube-system
-roleRef:
-  apiGroup: rbac.authorization.k8s.io
-  kind: Role
-  name: tiller-user
-subjects:
-- kind: ServiceAccount
-  name: default
-  namespace: molgenis-jenkins

molgenis-jenkins/resources/tiller-user-role.yaml

@@ -1,18 +0,0 @@
-apiVersion: rbac.authorization.k8s.io/v1beta1
-kind: Role
-metadata:
-  name: tiller-user
-  namespace: kube-system
-rules:
-- apiGroups:
-  - ""
-  resources:
-  - pods/portforward
-  verbs:
-  - create
-- apiGroups:
-  - ""
-  resources:
-  - pods
-  verbs:
-  - list

molgenis-jenkins/values.yaml

@@ -416,12 +416,6 @@ jenkins:
               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
@@ -453,69 +447,6 @@ jenkins:
               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

molgenis-opencpu/.helmignore

@@ -1,21 +0,0 @@
-# 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

molgenis-opencpu/Chart.yaml

@@ -1,8 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: Opencpu stack for MOLGENIS
-name: molgenis-opencpu
-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

molgenis-opencpu/README.md

@@ -1,38 +0,0 @@
-# MOLGENIS - OpenCPU Helm Chart
-
-NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
-
-## Containers
-
-This chart will deploy the following containers:
-
-- OpenCPU
-- MOLGENIS-httpd (to proxy the registry and docker to one domain)
-
-## Provisioning
-You can choose for the OpenCPU image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com. 
-You need to fill out 2 properties to determine which repository you are going to use.
-
-- ```opencpu.image.repository```
-- ```opencpu.image.tag```
-
-You can do this in the questions in Rancher or in the ```values.yaml```.
-
-
-
-## Development
-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.
-
-

molgenis-opencpu/questions.yml

@@ -1,28 +0,0 @@
-
-categories:
-- MOLGENIS
-questions:
-- variable: ingress.enabled
-  label: Enable ingress
-  default: false
-  description: "Enable ingress"
-  type: boolean
-  required: true
-  group: "Loadbalancing"
-- variable: opencpu.image.repository
-  label: Registry
-  default: "registry.hub.docker.com"
-  description: "Select a registry to pull from"
-  type: enum
-  options:
-  - "registry.hub.docker.com"
-  - "registry.molgenis.org"
-  required: true
-  group: "Provisioning"
-- variable: opencpu.image.tag
-  label: Version
-  default: ""
-  description: "Select a OpenCPU version (check the registry.molgenis.org or hub.docker.com for released tags)"
-  type: string
-  required: true
-  group: "Provisioning"

molgenis-opencpu/templates/_helpers.tpl

@@ -1,32 +0,0 @@
-{{/* vim: set filetype=mustache: */}}
-{{/*
-Expand the name of the chart.
-*/}}
-{{- define "opencpu.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 "opencpu.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 "opencpu.chart" -}}
-{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
-{{- end -}}

molgenis-opencpu/templates/deployment.yaml

@@ -1,35 +0,0 @@
-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 }}
-
-

molgenis-opencpu/templates/ingress.yaml

@@ -1,36 +0,0 @@
-{{- if .Values.ingress.enabled }}
-{{- range .Values.ingress.hosts }}
-apiVersion: extensions/v1beta1
-kind: Ingress
-metadata:
-  name: "{{ $.Release.Name }}-ingress"
-  labels:
-    app:  {{ $.Values.opencpu.name }}
-    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: {{ $.Values.opencpu.service.name }}
-            servicePort: {{ $.Values.opencpu.service.port }}
-{{- if .tls }}
-  tls:
-  - hosts:
-    - {{ .name }}
-    secretName: {{ .tlsSecret }}
-{{- end }}
----
-{{- end }}
-{{- end }}

molgenis-opencpu/templates/service.yaml

@@ -1,20 +0,0 @@
-apiVersion: v1
-kind: Service
-metadata:
-  name: {{ .Values.opencpu.service.name }}
-  labels:
-    app: {{ .Values.opencpu.service.name }}
-    release: {{ .Release.Name }}
-    heritage: {{ .Release.Service }}
-spec:
-  type: {{ .Values.opencpu.service.type }}
-  loadBalancerSourceRanges:
-  {{- range $index, $rule := .Values.opencpu.service.firewall }}
-    - {{ $rule }}
-  {{- end }}
-  ports:
-    - name: {{ .Values.opencpu.service.name }}
-      port: {{ .Values.opencpu.service.port }}
-  selector:
-    app: {{ template "opencpu.name" . }}
-    release: {{ .Release.Name }}

molgenis-opencpu/values.yaml

@@ -1,41 +0,0 @@
-# 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: {}