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

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Sido Haakma 2018-03-17 22:24:09 +01:00 committed by Gogs
parent 52ef079d0c bb0c6d2597
commit 3ba33df854
17 changed files with 292 additions and 197 deletions
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4
templates/molgenis/0/docker-compose.yml
View File

@ -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

11
templates/molgenis/1/README.md
View File

@ -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.

4
templates/molgenis/1/docker-compose.yml
View File

@ -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

26
templates/molgenis/2/README.md
View File

@ -1,17 +1,21 @@
# MOLGENIS
### Flexible software for scientific data
#### Process, manage, query, annotate, integrate, analyse, share
Flexible software for scientific data
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
- Postgress instance
- ElasticSearch instance
## Usage:
- MOLGENIS
- MOLGENIS-OpenCPU
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog
- Enter the name of the replica set
- Click deploy
- Fill in the questions in the template area
- 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.

49
templates/molgenis/2/docker-compose.yml
View File

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

2
templates/molgenis/2/rancher-compose.yml
View File

@ -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"

52
templates/molgenis/3/docker-compose.yml
View File

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

2
templates/molgenis/3/rancher-compose.yml
View File

@ -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"

11
templates/molgenis/4/README.md
View File

@ -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.

72
templates/molgenis/4/docker-compose.yml
View File

@ -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:${DOMAINS}
@ -19,22 +29,26 @@
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- POSTGRES_USER=${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:
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
- 9300:9300
# labels:
#io.rancher.sidekicks: elasticsearch-data
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0
ports:
- 8004:8004
- 9200
- 9300
volumes:
- elastic-data
labels:
io.rancher.scheduler.global: true
volumes:
postgres-data:
image: busybox
labels:
io.rancher.container.start_once: true
volumes:
- /var/lib/postgresql/data/pgdata
driver: local
molgenis-data:
image: busybox
labels:
io.rancher.container.start_once: true
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
driver: local
elastic-data:
driver: local

34
templates/molgenis/4/rancher-compose.yml
View File

@ -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
@ -25,4 +55,4 @@
unhealthy_threshold: 3
request_line: 'GET / HTTP/1.0'
healthy_threshold: 2
response_timeout: 5000
response_timeout: 5000

11
templates/molgenis/5/README.md
View File

@ -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.

67
templates/molgenis/5/docker-compose.yml
View File

@ -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:${DOMAINS}
@ -19,22 +29,26 @@
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- POSTGRES_USER=${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:
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
- 9300:9300
- 9200
- 9300
volumes:
- elastic-data
labels:
#io.rancher.sidekicks: elasticsearch-data
io.rancher.scheduler.global: true
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:6.0.0
ports:
- 8004:8004
volumes:
postgres-data:
image: busybox
labels:
io.rancher.container.start_once: true
volumes:
- /var/lib/postgresql/data/pgdata
driver: local
molgenis-data:
image: busybox
labels:
io.rancher.container.start_once: true
volumes:
- /opt/molgenis
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data
driver: local
elastic-data:
driver: local

34
templates/molgenis/5/rancher-compose.yml
View File

@ -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

11
templates/molgenis/6/README.md
View File

@ -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.

65
templates/molgenis/6/docker-compose.yml
View File

@ -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/${DB_SCHEME}?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
- "db_driver=org.postgresql.Driver"
- "db_user=molgenis"
- "db_password=molgenis"
- "admin.password=admin"
- "elasticsearch.cluster.name=molgenis"
- "db_user=${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:${DOMAINS}
@ -27,27 +29,26 @@
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- POSTGRES_USER=${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:
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
- 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
driver: local
molgenis-data:
image: busybox
labels:
io.rancher.container.start_once: true
volumes:
- /opt/molgenis
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data
driver: local
elastic-data:
driver: local

34
templates/molgenis/6/rancher-compose.yml
View File

@ -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