Merge branch 'master' of p281392/molgenis-ops-rancher into master
This commit is contained in:
commit
3ba33df854
@ -43,7 +43,7 @@ services:
|
|||||||
opencpu:
|
opencpu:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest
|
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest
|
||||||
ports:
|
ports:
|
||||||
- 8004:8004
|
- 8004
|
||||||
|
|
||||||
elasticsearch:
|
elasticsearch:
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
@ -66,7 +66,9 @@ services:
|
|||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
postgres-data:
|
postgres-data:
|
||||||
|
driver: local
|
||||||
molgenis-data:
|
molgenis-data:
|
||||||
|
driver: local
|
||||||
elastic-data:
|
elastic-data:
|
||||||
driver: local
|
driver: local
|
||||||
|
|
||||||
|
@ -2,15 +2,20 @@
|
|||||||
Flexible software for scientific data
|
Flexible software for scientific data
|
||||||
|
|
||||||
## Rancher configuration
|
## 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
|
||||||
|
- MOLGENIS-OpenCPU
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
- ElasticSearch
|
||||||
|
|
||||||
## Usage
|
## Usage
|
||||||
- Select MOLGENIS from catalog
|
- 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*
|
- 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.
|
||||||
|
|
||||||
|
@ -43,7 +43,7 @@ services:
|
|||||||
opencpu:
|
opencpu:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable
|
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable
|
||||||
ports:
|
ports:
|
||||||
- 8004:8004
|
- 8004
|
||||||
|
|
||||||
elasticsearch:
|
elasticsearch:
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
@ -66,7 +66,9 @@ services:
|
|||||||
|
|
||||||
volumes:
|
volumes:
|
||||||
postgres-data:
|
postgres-data:
|
||||||
|
driver: local
|
||||||
molgenis-data:
|
molgenis-data:
|
||||||
|
driver: local
|
||||||
elastic-data:
|
elastic-data:
|
||||||
driver: local
|
driver: local
|
||||||
|
|
||||||
|
@ -1,17 +1,21 @@
|
|||||||
# MOLGENIS
|
# 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
|
- 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.
|
|
@ -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: ${TRAEFIK_BACKEND}
|
||||||
traefik.enable: true
|
traefik.enable: true
|
||||||
traefik.port: 8080
|
traefik.port: 8080
|
||||||
db:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
|
postgres:
|
||||||
expose:
|
image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
|
||||||
- 5432
|
expose:
|
||||||
volumes:
|
- 5432
|
||||||
- db-data:/var/lib/postgresql/data
|
volumes:
|
||||||
|
- postgres-data:/var/lib/postgresql/data
|
||||||
|
|
||||||
|
volumes:
|
||||||
|
postgres-data:
|
||||||
|
molgenis-data:
|
||||||
|
elastic-data:
|
||||||
|
driver: local
|
@ -12,7 +12,7 @@
|
|||||||
type: "string"
|
type: "string"
|
||||||
- variable: "TRAEFIK_BACKEND"
|
- variable: "TRAEFIK_BACKEND"
|
||||||
description: "Name of the server when added to loadbalancer"
|
description: "Name of the server when added to loadbalancer"
|
||||||
label: "Backend:"
|
label: "Traefik backend:"
|
||||||
required: true
|
required: true
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
type: "string"
|
type: "string"
|
||||||
|
@ -1,20 +1,22 @@
|
|||||||
app:
|
version: '2'
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
|
services:
|
||||||
ports:
|
molgenis:
|
||||||
- 8081:8080
|
image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
|
||||||
links:
|
ports:
|
||||||
- db
|
- 8080
|
||||||
volumes_from:
|
links:
|
||||||
- molgenis-data
|
- postgres
|
||||||
labels:
|
volumes:
|
||||||
io.rancher.sidekicks: molgenis-data
|
- molgenis-data
|
||||||
io.rancher.scheduler.global: true
|
labels:
|
||||||
traefik.frontend.rule: Host:${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
|
image: postgres:9.6-alpine
|
||||||
environment:
|
environment:
|
||||||
- POSTGRES_USER=molgenis
|
- POSTGRES_USER=molgenis
|
||||||
@ -22,21 +24,13 @@ app:
|
|||||||
- POSTGRES_DB=molgenis
|
- POSTGRES_DB=molgenis
|
||||||
expose:
|
expose:
|
||||||
- 5432
|
- 5432
|
||||||
volumes_from:
|
volumes:
|
||||||
- postgres-data
|
- postgres-data
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: postgres-data
|
|
||||||
io.rancher.scheduler.global: true
|
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:
|
molgenis-data:
|
||||||
image: busybox
|
driver: local
|
||||||
labels:
|
postgres-data:
|
||||||
io.rancher.container.start_once: true
|
driver: local
|
||||||
volumes:
|
|
||||||
- /opt/molgenis
|
|
@ -12,7 +12,7 @@
|
|||||||
type: "string"
|
type: "string"
|
||||||
- variable: "TRAEFIK_BACKEND"
|
- variable: "TRAEFIK_BACKEND"
|
||||||
description: "Name of the server when added to loadbalancer"
|
description: "Name of the server when added to loadbalancer"
|
||||||
label: "Backend:"
|
label: "Traefik backend:"
|
||||||
required: true
|
required: true
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
type: "string"
|
type: "string"
|
||||||
|
@ -2,15 +2,20 @@
|
|||||||
Flexible software for scientific data
|
Flexible software for scientific data
|
||||||
|
|
||||||
## Rancher configuration
|
## 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
|
||||||
|
- MOLGENIS-OpenCPU
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
- ElasticSearch
|
||||||
|
|
||||||
## Usage
|
## Usage
|
||||||
- Select MOLGENIS from catalog
|
- 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*
|
- 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.
|
||||||
|
|
||||||
|
@ -1,3 +1,6 @@
|
|||||||
|
version: '2'
|
||||||
|
|
||||||
|
services:
|
||||||
molgenis:
|
molgenis:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
|
image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
|
||||||
ports:
|
ports:
|
||||||
@ -5,10 +8,17 @@
|
|||||||
links:
|
links:
|
||||||
- postgres
|
- postgres
|
||||||
- elasticsearch
|
- elasticsearch
|
||||||
volumes_from:
|
volumes:
|
||||||
- molgenis-data
|
- 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=${ELASTIC_CLUSTER}"
|
||||||
|
- "elasticsearch.transport.addresses=elasticsearch:9300"
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: molgenis-data
|
|
||||||
io.rancher.container.pull_image: always
|
io.rancher.container.pull_image: always
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
traefik.frontend.rule: Host:${DOMAINS}
|
||||||
@ -19,22 +29,26 @@
|
|||||||
postgres:
|
postgres:
|
||||||
image: postgres:9.6-alpine
|
image: postgres:9.6-alpine
|
||||||
environment:
|
environment:
|
||||||
- POSTGRES_USER=molgenis
|
- POSTGRES_USER=${DB_USERNAME}
|
||||||
- POSTGRES_PASSWORD=molgenis
|
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
||||||
- POSTGRES_DB=molgenis
|
- POSTGRES_DB=${DB_SCHEME}
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
- PGDATA=/var/lib/postgresql/data/pgdata
|
||||||
volumes_from:
|
volumes:
|
||||||
- postgres-data
|
- postgres-data
|
||||||
ports:
|
ports:
|
||||||
- 5432
|
- 5432
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: postgres-data
|
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
|
|
||||||
|
opencpu:
|
||||||
|
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0
|
||||||
|
ports:
|
||||||
|
- 8004
|
||||||
|
|
||||||
elasticsearch:
|
elasticsearch:
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
environment:
|
environment:
|
||||||
- "cluster.name=molgenis"
|
- "cluster.name=${ELASTIC_CLUSTER}"
|
||||||
- "bootstrap.memory_lock=true"
|
- "bootstrap.memory_lock=true"
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
||||||
- "xpack.security.enabled=false"
|
- "xpack.security.enabled=false"
|
||||||
@ -42,38 +56,18 @@
|
|||||||
memlock:
|
memlock:
|
||||||
soft: -1
|
soft: -1
|
||||||
hard: -1
|
hard: -1
|
||||||
# volumes_from:
|
|
||||||
# - elasticsearch-data
|
|
||||||
ports:
|
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:
|
postgres-data:
|
||||||
image: busybox
|
driver: local
|
||||||
labels:
|
|
||||||
io.rancher.container.start_once: true
|
|
||||||
volumes:
|
|
||||||
- /var/lib/postgresql/data/pgdata
|
|
||||||
|
|
||||||
molgenis-data:
|
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
|
|
@ -12,10 +12,40 @@
|
|||||||
type: "string"
|
type: "string"
|
||||||
- variable: "TRAEFIK_BACKEND"
|
- variable: "TRAEFIK_BACKEND"
|
||||||
description: "Name of the server when added to loadbalancer"
|
description: "Name of the server when added to loadbalancer"
|
||||||
label: "Backend:"
|
label: "Traefik backend:"
|
||||||
required: true
|
required: true
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
type: "string"
|
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
|
start_on_create: true
|
||||||
scale: 1
|
scale: 1
|
||||||
@ -25,4 +55,4 @@
|
|||||||
unhealthy_threshold: 3
|
unhealthy_threshold: 3
|
||||||
request_line: 'GET / HTTP/1.0'
|
request_line: 'GET / HTTP/1.0'
|
||||||
healthy_threshold: 2
|
healthy_threshold: 2
|
||||||
response_timeout: 5000
|
response_timeout: 5000
|
||||||
|
@ -2,15 +2,20 @@
|
|||||||
Flexible software for scientific data
|
Flexible software for scientific data
|
||||||
|
|
||||||
## Rancher configuration
|
## 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
|
||||||
|
- MOLGENIS-OpenCPU
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
- ElasticSearch
|
||||||
|
|
||||||
## Usage
|
## Usage
|
||||||
- Select MOLGENIS from catalog
|
- 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*
|
- 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.
|
||||||
|
|
||||||
|
@ -1,3 +1,6 @@
|
|||||||
|
version: '2'
|
||||||
|
|
||||||
|
services:
|
||||||
molgenis:
|
molgenis:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
|
image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
|
||||||
ports:
|
ports:
|
||||||
@ -5,10 +8,17 @@
|
|||||||
links:
|
links:
|
||||||
- postgres
|
- postgres
|
||||||
- elasticsearch
|
- elasticsearch
|
||||||
volumes_from:
|
volumes:
|
||||||
- molgenis-data
|
- 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=${ELASTIC_CLUSTER}"
|
||||||
|
- "elasticsearch.transport.addresses=elasticsearch:9300"
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: molgenis-data
|
|
||||||
io.rancher.container.pull_image: always
|
io.rancher.container.pull_image: always
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
traefik.frontend.rule: Host:${DOMAINS}
|
||||||
@ -19,22 +29,26 @@
|
|||||||
postgres:
|
postgres:
|
||||||
image: postgres:9.6-alpine
|
image: postgres:9.6-alpine
|
||||||
environment:
|
environment:
|
||||||
- POSTGRES_USER=molgenis
|
- POSTGRES_USER=${DB_USERNAME}
|
||||||
- POSTGRES_PASSWORD=molgenis
|
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
||||||
- POSTGRES_DB=molgenis
|
- POSTGRES_DB=${DB_SCHEME}
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
- PGDATA=/var/lib/postgresql/data/pgdata
|
||||||
volumes_from:
|
volumes:
|
||||||
- postgres-data
|
- postgres-data
|
||||||
ports:
|
ports:
|
||||||
- 5432
|
- 5432
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: postgres-data
|
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
|
|
||||||
|
opencpu:
|
||||||
|
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:6.0.0
|
||||||
|
ports:
|
||||||
|
- 8004
|
||||||
|
|
||||||
elasticsearch:
|
elasticsearch:
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
environment:
|
environment:
|
||||||
- "cluster.name=molgenis"
|
- "cluster.name=${ELASTIC_CLUSTER}"
|
||||||
- "bootstrap.memory_lock=true"
|
- "bootstrap.memory_lock=true"
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
||||||
- "xpack.security.enabled=false"
|
- "xpack.security.enabled=false"
|
||||||
@ -42,37 +56,18 @@
|
|||||||
memlock:
|
memlock:
|
||||||
soft: -1
|
soft: -1
|
||||||
hard: -1
|
hard: -1
|
||||||
# volumes_from:
|
|
||||||
# - elasticsearch-data
|
|
||||||
ports:
|
ports:
|
||||||
- 9200:9200
|
- 9200
|
||||||
- 9300:9300
|
- 9300
|
||||||
|
volumes:
|
||||||
|
- elastic-data
|
||||||
labels:
|
labels:
|
||||||
#io.rancher.sidekicks: elasticsearch-data
|
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
|
|
||||||
opencpu:
|
volumes:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:6.0.0
|
|
||||||
ports:
|
|
||||||
- 8004:8004
|
|
||||||
|
|
||||||
postgres-data:
|
postgres-data:
|
||||||
image: busybox
|
driver: local
|
||||||
labels:
|
|
||||||
io.rancher.container.start_once: true
|
|
||||||
volumes:
|
|
||||||
- /var/lib/postgresql/data/pgdata
|
|
||||||
|
|
||||||
molgenis-data:
|
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
|
|
@ -1,6 +1,6 @@
|
|||||||
.catalog:
|
.catalog:
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: v6.0.0
|
version: v6.0,0
|
||||||
description: Molgenis
|
description: Molgenis
|
||||||
minimum_rancher_version: v1.6.3
|
minimum_rancher_version: v1.6.3
|
||||||
questions:
|
questions:
|
||||||
@ -12,10 +12,40 @@
|
|||||||
type: "string"
|
type: "string"
|
||||||
- variable: "TRAEFIK_BACKEND"
|
- variable: "TRAEFIK_BACKEND"
|
||||||
description: "Name of the server when added to loadbalancer"
|
description: "Name of the server when added to loadbalancer"
|
||||||
label: "Backend:"
|
label: "Traefik backend:"
|
||||||
required: true
|
required: true
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
type: "string"
|
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
|
start_on_create: true
|
||||||
scale: 1
|
scale: 1
|
||||||
|
@ -2,15 +2,20 @@
|
|||||||
Flexible software for scientific data
|
Flexible software for scientific data
|
||||||
|
|
||||||
## Rancher configuration
|
## 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
|
||||||
|
- MOLGENIS-OpenCPU
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
- ElasticSearch
|
||||||
|
|
||||||
## Usage
|
## Usage
|
||||||
- Select MOLGENIS from catalog
|
- 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*
|
- 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.
|
||||||
|
|
||||||
|
@ -1,22 +1,24 @@
|
|||||||
|
version: '2'
|
||||||
|
|
||||||
|
services:
|
||||||
molgenis:
|
molgenis:
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0-SNAPSHOT
|
image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0
|
||||||
ports:
|
ports:
|
||||||
- 8080
|
- 8080
|
||||||
links:
|
links:
|
||||||
- postgres
|
- postgres
|
||||||
- elasticsearch
|
- elasticsearch
|
||||||
volumes_from:
|
volumes:
|
||||||
- molgenis-data
|
- molgenis-data
|
||||||
environment:
|
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_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=${ELASTIC_CLUSTER}"
|
||||||
- "elasticsearch.transport.addresses=elasticsearch:9300"
|
- "elasticsearch.transport.addresses=elasticsearch:9300"
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: molgenis-data
|
|
||||||
io.rancher.container.pull_image: always
|
io.rancher.container.pull_image: always
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
traefik.frontend.rule: Host:${DOMAINS}
|
||||||
@ -27,27 +29,26 @@
|
|||||||
postgres:
|
postgres:
|
||||||
image: postgres:9.6-alpine
|
image: postgres:9.6-alpine
|
||||||
environment:
|
environment:
|
||||||
- POSTGRES_USER=molgenis
|
- POSTGRES_USER=${DB_USERNAME}
|
||||||
- POSTGRES_PASSWORD=molgenis
|
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
||||||
- POSTGRES_DB=molgenis
|
- POSTGRES_DB=${DB_SCHEME}
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
- PGDATA=/var/lib/postgresql/data/pgdata
|
||||||
volumes_from:
|
volumes:
|
||||||
- postgres-data
|
- postgres-data
|
||||||
ports:
|
ports:
|
||||||
- 5432
|
- 5432
|
||||||
labels:
|
labels:
|
||||||
io.rancher.sidekicks: postgres-data
|
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
|
|
||||||
opencpu:
|
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:
|
ports:
|
||||||
- 8004:8004
|
- 8004
|
||||||
|
|
||||||
elasticsearch:
|
elasticsearch:
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
environment:
|
environment:
|
||||||
- "cluster.name=molgenis"
|
- "cluster.name=${ELASTIC_CLUSTER}"
|
||||||
- "bootstrap.memory_lock=true"
|
- "bootstrap.memory_lock=true"
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
||||||
- "xpack.security.enabled=false"
|
- "xpack.security.enabled=false"
|
||||||
@ -55,32 +56,18 @@
|
|||||||
memlock:
|
memlock:
|
||||||
soft: -1
|
soft: -1
|
||||||
hard: -1
|
hard: -1
|
||||||
# volumes_from:
|
|
||||||
# - elasticsearch-data
|
|
||||||
ports:
|
ports:
|
||||||
- 9200:9200
|
- 9200
|
||||||
- 9300:9300
|
- 9300
|
||||||
|
volumes:
|
||||||
|
- elastic-data
|
||||||
labels:
|
labels:
|
||||||
#io.rancher.sidekicks: elasticsearch-data
|
|
||||||
io.rancher.scheduler.global: true
|
io.rancher.scheduler.global: true
|
||||||
|
|
||||||
|
volumes:
|
||||||
postgres-data:
|
postgres-data:
|
||||||
image: busybox
|
driver: local
|
||||||
labels:
|
|
||||||
io.rancher.container.start_once: true
|
|
||||||
volumes:
|
|
||||||
- /var/lib/postgresql/data/pgdata
|
|
||||||
|
|
||||||
molgenis-data:
|
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
|
|
@ -1,6 +1,6 @@
|
|||||||
.catalog:
|
.catalog:
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: v7.0.0
|
version: v6.0,0
|
||||||
description: Molgenis
|
description: Molgenis
|
||||||
minimum_rancher_version: v1.6.3
|
minimum_rancher_version: v1.6.3
|
||||||
questions:
|
questions:
|
||||||
@ -12,10 +12,40 @@
|
|||||||
type: "string"
|
type: "string"
|
||||||
- variable: "TRAEFIK_BACKEND"
|
- variable: "TRAEFIK_BACKEND"
|
||||||
description: "Name of the server when added to loadbalancer"
|
description: "Name of the server when added to loadbalancer"
|
||||||
label: "Backend:"
|
label: "Traefik backend:"
|
||||||
required: true
|
required: true
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
type: "string"
|
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
|
start_on_create: true
|
||||||
scale: 1
|
scale: 1
|
||||||
|
Loading…
Reference in New Issue
Block a user