feat(docker-compose): updated all volumes to local drivers

templates/molgenis/0/docker-compose.yml

@@ -43,7 +43,7 @@ services:
   opencpu:
     image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest
     ports:
-      - 8004:8004
+      - 8004
 
   elasticsearch:
     image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
@@ -66,7 +66,9 @@ services:
 
 volumes:
   postgres-data:
+    driver: local
   molgenis-data:
+    driver: local
   elastic-data:
     driver: local
 

templates/molgenis/1/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/1/docker-compose.yml

@@ -43,7 +43,7 @@ services:
   opencpu:
     image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable
     ports:
-      - 8004:8004
+      - 8004
 
   elasticsearch:
     image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
@@ -66,7 +66,9 @@ services:
 
 volumes:
   postgres-data:
+    driver: local
   molgenis-data:
+    driver: local
   elastic-data:
     driver: local
 

templates/molgenis/2/README.md

@@ -1,17 +1,21 @@
 # MOLGENIS
-### Flexible software for scientific data
+Flexible software for scientific data
-#### Process, manage, query, annotate, integrate, analyse, share
 
-This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
+## Rancher configuration
+These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
 
-- MOLGENIS instance
+- MOLGENIS
-- Postgress instance
+- MOLGENIS-OpenCPU
-- ElasticSearch instance
+- Postgress
-
+- ElasticSearch
-## Usage:
 
+## Usage
 - Select MOLGENIS from catalog
-- Enter the name of the replica set
+- Fill in the questions in the template area 
-- Click deploy
+- Click *Launch*
+
+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.
 
-MOLGENIS can now be accessed over the Rancher network.

templates/molgenis/2/docker-compose.yml

@@ -1,21 +1,28 @@
-app:
+services:
-  image: registry.webhosting.rug.nl/molgenis:2.0.1
+  molgenis:
-  ports:
+    image: registry.webhosting.rug.nl/molgenis:2.0.1
-    - 8081:8080
+    ports:
-  links:
+      - 8080
-    - db
+    links:
-  volumes:
+      - db
-    - app-data:/opt/molgenis
+    volumes:
-  labels:
+      - molgenis-data:/opt/molgenis
-    io.rancher.container.create_agent: true
+    labels:
-    io.rancher.scheduler.global: true
+      io.rancher.scheduler.global: true
-    traefik.frontend.rule: Host:${DOMAINS}
+      traefik.frontend.rule: Host:${DOMAINS}
-    traefik.backend: ${TRAEFIK_BACKEND}
+      traefik.backend: ${TRAEFIK_BACKEND}
-    traefik.enable: true
+      traefik.enable: true
-    traefik.port: 8080
+      traefik.port: 8080
-db:
+
-  image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
+  postgres:
-  expose:
+    image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
-    - 5432
+    expose:
-  volumes:
+      - 5432
-    - db-data:/var/lib/postgresql/data
+    volumes:
+      - postgres-data:/var/lib/postgresql/data
+
+volumes:
+  postgres-data:
+  molgenis-data:
+  elastic-data:
+    driver: local

templates/molgenis/2/rancher-compose.yml

@@ -12,7 +12,7 @@
       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"

templates/molgenis/3/docker-compose.yml

@@ -1,20 +1,22 @@
-app:
+version: '2'
-  image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
+services:
-  ports:
+  molgenis:
-    - 8081:8080
+    image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
-  links:
+    ports:
-    - db
+      - 8080
-  volumes_from:
+    links:
-    - molgenis-data
+      - postgres
-  labels:
+    volumes:
-    io.rancher.sidekicks: molgenis-data
+      - molgenis-data
-    io.rancher.scheduler.global: true
+    labels:
-    traefik.frontend.rule: Host:${DOMAINS}
+      io.rancher.sidekicks: molgenis-data
-    traefik.backend: ${TRAEFIK_BACKEND}
+      io.rancher.scheduler.global: true
-    traefik.enable: true
+      traefik.frontend.rule: Host:${DOMAINS}
-    traefik.port: 8080
+      traefik.backend: ${TRAEFIK_BACKEND}
+      traefik.enable: true
+      traefik.port: 8080
 
-  db:
+  postgres:
     image: postgres:9.6-alpine
     environment:
       - POSTGRES_USER=molgenis
@@ -22,21 +24,13 @@ app:
       - POSTGRES_DB=molgenis
     expose:
       - 5432
-     volumes_from:
+    volumes:
       - postgres-data
     labels:
-      io.rancher.sidekicks: postgres-data
       io.rancher.scheduler.global: true
 
- postgres-data:
+volumes:
-    image: busybox
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /var/lib/postgresql/data/pgdata
   molgenis-data:
-    image: busybox
+    driver: local
-    labels:
+  postgres-data:
-      io.rancher.container.start_once: true
+    driver: local
-    volumes:
-      - /opt/molgenis

templates/molgenis/3/rancher-compose.yml

@@ -12,7 +12,7 @@
       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"

templates/molgenis/4/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/4/docker-compose.yml

@@ -1,3 +1,6 @@
+version: '2'
+
+services:
   molgenis:
     image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
     ports:
@@ -5,10 +8,17 @@
     links:
       - postgres
       - elasticsearch
-    volumes_from:
+    volumes:
       - molgenis-data
+    environment:
+      - "db_uri=jdbc:postgresql://postgres/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
+      - "db_driver=org.postgresql.Driver"
+      - "db_user=${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:${DOMAINS}
@@ -19,22 +29,26 @@
   postgres:
     image: postgres:9.6-alpine
     environment:
-      - POSTGRES_USER=molgenis
+      - POSTGRES_USER=${DB_USERNAME}
-      - POSTGRES_PASSWORD=molgenis
+      - POSTGRES_PASSWORD=${DB_PASSWORD}
-      - POSTGRES_DB=molgenis
+      - POSTGRES_DB=${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:
+    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0
+    ports:
+      - 8004
+
   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"
@@ -42,38 +56,18 @@
       memlock:
         soft: -1
         hard: -1
-#    volumes_from:
-#      - elasticsearch-data
     ports:
-       - 9200:9200
+       - 9200
-       - 9300:9300
+       - 9300
-#    labels:
+    volumes:
-      #io.rancher.sidekicks: elasticsearch-data
+       - elastic-data
-
+    labels:
-  opencpu:
+      io.rancher.scheduler.global: true
-    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0
-    ports:
-      - 8004:8004
 
+volumes:
   postgres-data:
-    image: busybox
+    driver: local
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /var/lib/postgresql/data/pgdata
-
   molgenis-data:
-    image: busybox
+    driver: local
-    labels:
+  elastic-data:
-      io.rancher.container.start_once: true
+    driver: local
-    volumes:
-      - /opt/molgenis
-
-#  elasticsearch-data:
-#    image: busybox
-#    labels:
-#      io.rancher.container.start_once: true
-#      io.rancher.scheduler.affinity:host_label: type=molgenis
-#      io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
-#    volumes:
-#      - /usr/share/elasticsearch/data

templates/molgenis/4/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

templates/molgenis/5/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/5/docker-compose.yml

@@ -1,3 +1,6 @@
+version: '2'
+
+services:
   molgenis:
     image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
     ports:
@@ -5,10 +8,17 @@
     links:
       - postgres
       - elasticsearch
-    volumes_from:
+    volumes:
       - molgenis-data
+    environment:
+      - "db_uri=jdbc:postgresql://postgres/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
+      - "db_driver=org.postgresql.Driver"
+      - "db_user=${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:${DOMAINS}
@@ -19,22 +29,26 @@
   postgres:
     image: postgres:9.6-alpine
     environment:
-      - POSTGRES_USER=molgenis
+      - POSTGRES_USER=${DB_USERNAME}
-      - POSTGRES_PASSWORD=molgenis
+      - POSTGRES_PASSWORD=${DB_PASSWORD}
-      - POSTGRES_DB=molgenis
+      - POSTGRES_DB=${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:
+    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:6.0.0
+    ports:
+      - 8004
+
   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"
@@ -42,37 +56,18 @@
       memlock:
         soft: -1
         hard: -1
-#    volumes_from:
-#      - elasticsearch-data
     ports:
-       - 9200:9200
+       - 9200
-       - 9300:9300
+       - 9300
+    volumes:
+       - elastic-data
     labels:
-      #io.rancher.sidekicks: elasticsearch-data
       io.rancher.scheduler.global: true
 
-  opencpu:
+volumes:
-    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:6.0.0
-    ports:
-      - 8004:8004
-
   postgres-data:
-    image: busybox
+    driver: local
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /var/lib/postgresql/data/pgdata
-
   molgenis-data:
-    image: busybox
+    driver: local
-    labels:
+  elastic-data:
-      io.rancher.container.start_once: true
+    driver: local
-    volumes:
-      - /opt/molgenis
-
-#  elasticsearch-data:
-#    image: busybox
-#    labels:
-#      io.rancher.container.start_once: true
-#    volumes:
-#      - /usr/share/elasticsearch/data

templates/molgenis/5/rancher-compose.yml

@@ -1,6 +1,6 @@
 .catalog:
   name: molgenis
-  version: v6.0.0
+  version: v6.0,0
   description: Molgenis
   minimum_rancher_version: v1.6.3
   questions:
@@ -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

templates/molgenis/6/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/6/docker-compose.yml

@@ -1,22 +1,24 @@
+version: '2'
+
+services:
   molgenis:
-    image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0-SNAPSHOT
+    image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0
     ports:
       - 8080
     links:
       - postgres
       - elasticsearch
-    volumes_from:
+    volumes:
       - molgenis-data
     environment:
-      - "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
+      - "db_uri=jdbc:postgresql://postgres/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
       - "db_driver=org.postgresql.Driver"
-      - "db_user=molgenis"
+      - "db_user=${DB_USERNAME}"
-      - "db_password=molgenis"
+      - "db_password=${DB_PASSWORD}"
-      - "admin.password=admin"
+      - "admin.password={MOLGENIS_ADMIN_PASSWORD}"
-      - "elasticsearch.cluster.name=molgenis"
+      - "elasticsearch.cluster.name=${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:${DOMAINS}
@@ -27,27 +29,26 @@
   postgres:
     image: postgres:9.6-alpine
     environment:
-      - POSTGRES_USER=molgenis
+      - POSTGRES_USER=${DB_USERNAME}
-      - POSTGRES_PASSWORD=molgenis
+      - POSTGRES_PASSWORD=${DB_PASSWORD}
-      - POSTGRES_DB=molgenis
+      - POSTGRES_DB=${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:
-    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:7.0.0-SNAPSHOT
+    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:7.0.0
     ports:
-      - 8004:8004
+      - 8004
 
   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 +56,18 @@
       memlock:
         soft: -1
         hard: -1
-#    volumes_from:
-#      - elasticsearch-data
     ports:
-       - 9200:9200
+       - 9200
-       - 9300:9300
+       - 9300
+    volumes:
+       - elastic-data
     labels:
-      #io.rancher.sidekicks: elasticsearch-data
       io.rancher.scheduler.global: true
 
+volumes:
   postgres-data:
-    image: busybox
+    driver: local
-    labels:
-      io.rancher.container.start_once: true
-    volumes:
-      - /var/lib/postgresql/data/pgdata
-
   molgenis-data:
-    image: busybox
+    driver: local
-    labels:
+  elastic-data:
-      io.rancher.container.start_once: true
+    driver: local
-    volumes:
-      - /opt/molgenis
-
-#  elasticsearch-data:
-#    image: busybox
-#    labels:
-#      io.rancher.container.start_once: true
-#    volumes:
-#      - /usr/share/elasticsearch/data

templates/molgenis/6/rancher-compose.yml

@@ -1,6 +1,6 @@
 .catalog:
   name: molgenis
-  version: v7.0.0
+  version: v6.0,0
   description: Molgenis
   minimum_rancher_version: v1.6.3
   questions:
@@ -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