Merge branch 'master' of p281392/molgenis-ops-rancher into master

templates/molgenis/0/README.md

@@ -2,15 +2,20 @@
 Flexible software for scientific data
 
 ## Rancher configuration
-This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
+These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
 
 - MOLGENIS
+- MOLGENIS-OpenCPU
 - Postgress
 - ElasticSearch
 
 ## Usage
 - Select MOLGENIS from catalog
-- The stack-name must not be altered (this is hardcoded in de docker-compose file) 
+- Fill in the questions in the template area 
 - Click *Launch*
 
-MOLGENIS can now be accessed over the Rancher network.
+MOLGENIS can now be accessed over the Rancher network on the domains you specified.
+
+## Loadbalancers
+You can check lb.molgenis.org to check the availabity of the stack.
+

templates/molgenis/0/docker-compose.yml

@@ -13,7 +13,7 @@ services:
     environment:
       - "db_uri=jdbc:postgresql://postgres/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
       - "db_driver=org.postgresql.Driver"
-      - "db_user=${DB_USER}"
+      - "db_user=${DB_USERNAME}"
       - "db_password=${DB_PASSWORD}"
       - "admin.password={MOLGENIS_ADMIN_PASSWORD}"
       - "elasticsearch.cluster.name=${ELASTIC_CLUSTER}"
@@ -29,7 +29,7 @@ services:
   postgres:
     image: postgres:9.6-alpine
     environment:
-      - POSTGRES_USER=${DB_USER}
+      - POSTGRES_USER=${DB_USERNAME}
       - POSTGRES_PASSWORD=${DB_PASSWORD}
       - POSTGRES_DB=${DB_SCHEME}
       - PGDATA=/var/lib/postgresql/data/pgdata

templates/molgenis/0/rancher-compose.yml

@@ -22,7 +22,7 @@
       required: true
       default: "molgenis"
       type: "string"
-    - variable: "DB_USER_NAME"
+    - variable: "DB_USERNAME"
       description: "Name of the database username"
       label: "Database username:"
       required: true

templates/molgenis/1/docker-compose.yml

@@ -1,3 +1,6 @@
+version: '2'
+
+services:
   molgenis:
     image: registry.webhosting.rug.nl/molgenis/molgenis:stable
     ports:
@@ -5,18 +8,17 @@
     links:
       - postgres
       - elasticsearch
-    volumes_from:
+    volumes:
       - molgenis-data
     environment:
-      - "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
+      - "db_uri=jdbc:postgresql://postgres/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
       - "db_driver=org.postgresql.Driver"
-      - "db_user=molgenis"
-      - "db_password=molgenis"
-      - "admin.password=admin"
-      - "elasticsearch.cluster.name=molgenis"
+      - "db_user=${DB_USERNAME}"
+      - "db_password=${DB_PASSWORD}"
+      - "admin.password={MOLGENIS_ADMIN_PASSWORD}"
+      - "elasticsearch.cluster.name=${ELASTIC_CLUSTER}"
       - "elasticsearch.transport.addresses=elasticsearch:9300"
     labels:
-      io.rancher.sidekicks: molgenis-data
       io.rancher.container.pull_image: always
       io.rancher.scheduler.global: true
       traefik.frontend.rule: Host:${DOMAINS}
@@ -27,16 +29,15 @@
   postgres:
     image: postgres:9.6-alpine
     environment:
-      - POSTGRES_USER=molgenis
-      - POSTGRES_PASSWORD=molgenis
-      - POSTGRES_DB=molgenis
+      - POSTGRES_USER=${DB_USERNAME}
+      - POSTGRES_PASSWORD=${DB_PASSWORD}
+      - POSTGRES_DB=${DB_SCHEME}
       - PGDATA=/var/lib/postgresql/data/pgdata
-    volumes_from:
+    volumes:
       - postgres-data
     ports:
       - 5432
     labels:
-      io.rancher.sidekicks: postgres-data
       io.rancher.scheduler.global: true
 
   opencpu:
@@ -47,7 +48,7 @@
   elasticsearch:
     image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
     environment:
-      - "cluster.name=molgenis"
+      - "cluster.name=${ELASTIC_CLUSTER}"
       - "bootstrap.memory_lock=true"
       - "ES_JAVA_OPTS=-Xms1g -Xmx1g"
       - "xpack.security.enabled=false"
@@ -55,32 +56,17 @@
       memlock:
         soft: -1
         hard: -1
-#    volumes_from:
-#      - elasticsearch-data
     ports:
-       - 9200:9200
-       - 9300:9300
+       - 9200
+       - 9300
+    volumes:
+       - elastic-data
     labels:
-      #io.rancher.sidekicks: elasticsearch-data
       io.rancher.scheduler.global: true
 
+volumes:
   postgres-data:
-    image: busybox
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /var/lib/postgresql/data/pgdata
-
   molgenis-data:
-    image: busybox
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /opt/molgenis
+  elastic-data:
+    driver: local
 
-#  elasticsearch-data:
-#    image: busybox
-#    labels:
-#      io.rancher.container.start_once: true
-#    volumes:
-#      - /usr/share/elasticsearch/data

templates/molgenis/1/rancher-compose.yml

@@ -12,10 +12,40 @@
       type: "string"
     - variable: "TRAEFIK_BACKEND"
       description: "Name of the server when added to loadbalancer"
-      label: "Backend:"
+      label: "Traefik backend:"
       required: true
       default: "test.molgenis.org"
       type: "string"
+    - variable: "DB_SCHEME"
+      description: "Name of the database scheme"
+      label: "Database scheme:"
+      required: true
+      default: "molgenis"
+      type: "string"
+    - variable: "DB_USERNAME"
+      description: "Name of the database username"
+      label: "Database username:"
+      required: true
+      default: "molgenis"
+      type: "string"
+    - variable: "DB_PASSWORD"
+      description: "Password of the database user"
+      label: "Database password:"
+      required: true
+      default: "molgenis"
+      type: "string"
+    - variable: "MOLGENIS_ADMIN_PASSWORD"
+      description: "Passowrd the MOLGENIS admin"
+      label: "MOLGENIS admin user password:"
+      required: true
+      default: "admin"
+      type: "string"
+    - variable: "ELASTIC_CLUSTER"
+      description: "Name of the elasticsearch cluster"
+      label: "Cluster:"
+      required: true
+      default: "molgenis"
+      type: "string"
 
   start_on_create: true
   scale: 1