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17
templates/molgenis/0/README.md
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@ -1,17 +1,16 @@
# MOLGENIS
### Flexible software for scientific data
#### Process, manage, query, annotate, integrate, analyse, share
Flexible software for scientific data
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS instance
- Postgress instance
- ElasticSearch instance
## Usage:
- MOLGENIS
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog
- Enter the name of the replica set
- Click deploy
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
- Click *Launch*
MOLGENIS can now be accessed over the Rancher network.

86
templates/molgenis/0/docker-compose.yml
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@ -1,21 +1,85 @@
app:
image: registry.webhosting.rug.nl/molgenis:2.0.1
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:stable
ports:
- 8081:8080
- 8080
links:
- db
volumes:
- app-data:/opt/molgenis
- postgres
- elasticsearch
volumes_from:
- molgenis-data
environment:
- "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
- "db_driver=org.postgresql.Driver"
- "db_user=molgenis"
- "db_password=molgenis"
- "elasticsearch.cluster.name=molgenis"
- "elasticsearch.transport.addresses=elasticsearch:9300"
labels:
io.rancher.container.create_agent: true
io.rancher.sidekicks: molgenis-data
io.rancher.container.pull_image: always
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:
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- PGDATA=/var/lib/postgresql/data/pgdata
volumes_from:
- postgres-data
ports:
- 5432
labels:
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable
ports:
- 8004:8004
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
memlock:
soft: -1
hard: -1
# volumes_from:
# - elasticsearch-data
ports:
- 9200:9200
- 9300:9300
labels:
#io.rancher.sidekicks: elasticsearch-data
io.rancher.scheduler.global: true
postgres-data:
image: busybox
labels:
io.rancher.container.start_once: true
volumes:
- db-data:/var/lib/postgresql/data
- /var/lib/postgresql/data/pgdata
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

2
templates/molgenis/0/rancher-compose.yml
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@ -1,6 +1,6 @@
.catalog:
name: molgenis
version: v2.0.0
version: latest
description: Molgenis
minimum_rancher_version: v1.6.3
questions:

3
templates/molgenis/1/README.md
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@ -1,13 +1,12 @@
# MOLGENIS
Flexible software for scientific data
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS
- Elasticsearch is packaged with MOLGENIS
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog

57
templates/molgenis/1/docker-compose.yml
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@ -1,42 +1,85 @@
app:
image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:latest
ports:
- 8081:8080
- 8080
links:
- db
- postgres
- elasticsearch
volumes_from:
- molgenis-data
environment:
- "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
- "db_driver=org.postgresql.Driver"
- "db_user=molgenis"
- "db_password=molgenis"
- "elasticsearch.cluster.name=molgenis"
- "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}
traefik.backend: ${TRAEFIK_BACKEND}
traefik.enable: true
traefik.port: 8080
db:
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
expose:
- 5432
- PGDATA=/var/lib/postgresql/data/pgdata
volumes_from:
- postgres-data
ports:
- 5432
labels:
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest
ports:
- 8004:8004
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
memlock:
soft: -1
hard: -1
# volumes_from:
# - elasticsearch-data
ports:
- 9200:9200
- 9300:9300
labels:
#io.rancher.sidekicks: elasticsearch-data
io.rancher.scheduler.global: true
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
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data

2
templates/molgenis/1/rancher-compose.yml
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@ -1,6 +1,6 @@
.catalog:
name: molgenis
version: v4.1.0
version: stable
description: Molgenis
minimum_rancher_version: v1.6.3
questions:

17
templates/molgenis/2/README.md
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@ -1,16 +1,17 @@
# MOLGENIS
Flexible software for scientific data
### Flexible software for scientific data
#### Process, manage, query, annotate, integrate, analyse, share
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS
- Postgress
- ElasticSearch
- MOLGENIS instance
- Postgress instance
- ElasticSearch instance
## Usage:
## Usage
- Select MOLGENIS from catalog
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
- Click *Launch*
- Enter the name of the replica set
- Click deploy
MOLGENIS can now be accessed over the Rancher network.

80
templates/molgenis/2/docker-compose.yml
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@ -1,79 +1,21 @@
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
app:
image: registry.webhosting.rug.nl/molgenis:2.0.1
ports:
- 8080
- 8081:8080
links:
- postgres
- elasticsearch
volumes_from:
- molgenis-data
- db
volumes:
- app-data:/opt/molgenis
labels:
io.rancher.sidekicks: molgenis-data
io.rancher.container.pull_image: always
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
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- PGDATA=/var/lib/postgresql/data/pgdata
volumes_from:
- postgres-data
ports:
db:
image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
expose:
- 5432
labels:
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
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
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
# 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
- db-data:/var/lib/postgresql/data

2
templates/molgenis/2/rancher-compose.yml
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@ -1,6 +1,6 @@
.catalog:
name: molgenis
version: v5.2.0
version: v2.0.0
description: Molgenis
minimum_rancher_version: v1.6.3
questions:

3
templates/molgenis/3/README.md
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@ -1,12 +1,13 @@
# MOLGENIS
Flexible software for scientific data
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS
- Elasticsearch is packaged with MOLGENIS
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog

50
templates/molgenis/3/docker-compose.yml
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@ -1,78 +1,42 @@
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
app:
image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
ports:
- 8080
- 8081:8080
links:
- postgres
- elasticsearch
- db
volumes_from:
- molgenis-data
labels:
io.rancher.sidekicks: molgenis-data
io.rancher.container.pull_image: always
io.rancher.scheduler.global: true
traefik.frontend.rule: Host:${DOMAINS}
traefik.backend: ${TRAEFIK_BACKEND}
traefik.enable: true
traefik.port: 8080
postgres:
db:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- PGDATA=/var/lib/postgresql/data/pgdata
expose:
- 5432
volumes_from:
- postgres-data
ports:
- 5432
labels:
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
memlock:
soft: -1
hard: -1
# volumes_from:
# - elasticsearch-data
ports:
- 9200:9200
- 9300:9300
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
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
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data

2
templates/molgenis/3/rancher-compose.yml
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@ -1,6 +1,6 @@
.catalog:
name: molgenis
version: v6.0.0
version: v4.1.0
description: Molgenis
minimum_rancher_version: v1.6.3
questions:

24
templates/molgenis/4/docker-compose.yml
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@ -1,5 +1,5 @@
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0-SNAPSHOT
image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
ports:
- 8080
links:
@ -7,13 +7,6 @@
- elasticsearch
volumes_from:
- molgenis-data
environment:
- "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
- "db_driver=org.postgresql.Driver"
- "db_user=molgenis"
- "db_password=molgenis"
- "elasticsearch.cluster.name=molgenis"
- "elasticsearch.transport.addresses=elasticsearch:9300"
labels:
io.rancher.sidekicks: molgenis-data
io.rancher.container.pull_image: always
@ -38,11 +31,6 @@
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:7.0.0-SNAPSHOT
ports:
- 8004:8004
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
@ -59,9 +47,13 @@
ports:
- 9200:9200
- 9300:9300
labels:
# labels:
#io.rancher.sidekicks: elasticsearch-data
io.rancher.scheduler.global: true
opencpu:
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0
ports:
- 8004:8004
postgres-data:
image: busybox
@ -81,5 +73,7 @@
# 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

2
templates/molgenis/4/rancher-compose.yml
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@ -1,6 +1,6 @@
.catalog:
name: molgenis
version: v7.0.0
version: v5.2.0
description: Molgenis
minimum_rancher_version: v1.6.3
questions:

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templates/molgenis/5/README.md Normal file
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@ -0,0 +1,16 @@
# MOLGENIS
Flexible software for scientific data
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
- Click *Launch*
MOLGENIS can now be accessed over the Rancher network.

78
templates/molgenis/5/docker-compose.yml Normal file
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molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
ports:
- 8080
links:
- postgres
- elasticsearch
volumes_from:
- molgenis-data
labels:
io.rancher.sidekicks: molgenis-data
io.rancher.container.pull_image: always
io.rancher.scheduler.global: true
traefik.frontend.rule: Host:${DOMAINS}
traefik.backend: ${TRAEFIK_BACKEND}
traefik.enable: true
traefik.port: 8080
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- PGDATA=/var/lib/postgresql/data/pgdata
volumes_from:
- postgres-data
ports:
- 5432
labels:
io.rancher.sidekicks: postgres-data
io.rancher.scheduler.global: true
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
memlock:
soft: -1
hard: -1
# volumes_from:
# - elasticsearch-data
ports:
- 9200:9200
- 9300:9300
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
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
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data

28
templates/molgenis/5/rancher-compose.yml Normal file
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.catalog:
name: molgenis
version: v6.0.0
description: Molgenis
minimum_rancher_version: v1.6.3
questions:
- variable: "DOMAINS"
description: "Domain you want to use (comma seperated)"
label: "Domains:"
required: true
default: "test.molgenis.org,test.dcktest.gcc.rug.nl"
type: "string"
- variable: "TRAEFIK_BACKEND"
description: "Name of the server when added to loadbalancer"
label: "Backend:"
required: true
default: "test.molgenis.org"
type: "string"
start_on_create: true
scale: 1
health_check:
port: 8080
interval: 5000
unhealthy_threshold: 3
request_line: 'GET / HTTP/1.0'
healthy_threshold: 2
response_timeout: 5000

16
templates/molgenis/6/README.md Normal file
View File

@ -0,0 +1,16 @@
# MOLGENIS
Flexible software for scientific data
## Rancher configuration
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
- MOLGENIS
- Postgress
- ElasticSearch
## Usage
- Select MOLGENIS from catalog
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
- Click *Launch*
MOLGENIS can now be accessed over the Rancher network.

85
templates/molgenis/6/docker-compose.yml Normal file
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@ -0,0 +1,85 @@
molgenis:
image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0-SNAPSHOT
ports:
- 8080
links:
- postgres
- elasticsearch
volumes_from:
- molgenis-data
environment:
- "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE"
- "db_driver=org.postgresql.Driver"
- "db_user=molgenis"
- "db_password=molgenis"
- "elasticsearch.cluster.name=molgenis"
- "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}
traefik.backend: ${TRAEFIK_BACKEND}
traefik.enable: true
traefik.port: 8080
postgres:
image: postgres:9.6-alpine
environment:
- POSTGRES_USER=molgenis
- POSTGRES_PASSWORD=molgenis
- POSTGRES_DB=molgenis
- PGDATA=/var/lib/postgresql/data/pgdata
volumes_from:
- 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
ports:
- 8004:8004
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
environment:
- "cluster.name=molgenis"
- "bootstrap.memory_lock=true"
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
- "xpack.security.enabled=false"
ulimits:
memlock:
soft: -1
hard: -1
# volumes_from:
# - elasticsearch-data
ports:
- 9200:9200
- 9300:9300
labels:
#io.rancher.sidekicks: elasticsearch-data
io.rancher.scheduler.global: true
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
# elasticsearch-data:
# image: busybox
# labels:
# io.rancher.container.start_once: true
# volumes:
# - /usr/share/elasticsearch/data

28
templates/molgenis/6/rancher-compose.yml Normal file
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@ -0,0 +1,28 @@
.catalog:
name: molgenis
version: v7.0.0
description: Molgenis
minimum_rancher_version: v1.6.3
questions:
- variable: "DOMAINS"
description: "Domain you want to use (comma seperated)"
label: "Domains:"
required: true
default: "test.molgenis.org,test.dcktest.gcc.rug.nl"
type: "string"
- variable: "TRAEFIK_BACKEND"
description: "Name of the server when added to loadbalancer"
label: "Backend:"
required: true
default: "test.molgenis.org"
type: "string"
start_on_create: true
scale: 1
health_check:
port: 8080
interval: 5000
unhealthy_threshold: 3
request_line: 'GET / HTTP/1.0'
healthy_threshold: 2
response_timeout: 5000