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README.md
12
README.md
@ -1,12 +0,0 @@
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|||||||
# Rancher
|
|
||||||
We use docker-compose.yml files to specify a version-range to deploy a MOLGENIS-stack
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||||||
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||||||
## Configuration
|
|
||||||
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|
||||||
Exmaple
|
|
||||||
|
|
||||||
```bash
|
|
||||||
molgenis:
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|
||||||
image: registry.webhosting.rug.nl/molgenis-docker:5.2.0
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|
||||||
```
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|
||||||
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|
||||||
@ -1,17 +0,0 @@
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|||||||
# Jenkins for MOLGENIS
|
|
||||||
Flexible software for scientific data
|
|
||||||
|
|
||||||
## Rancher configuration
|
|
||||||
These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
|
|
||||||
|
|
||||||
- Jenkins
|
|
||||||
- Jenkins Agent - Development tools
|
|
||||||
|
|
||||||
## Usage
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|
||||||
- Select Jenkins from catalog
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||||||
- Fill in the questions in the template area
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|
||||||
- Click *Launch*
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|
||||||
|
|
||||||
## Loadbalancers
|
|
||||||
You can check lb.molgenis.org to check the availabity of the stack.
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|
||||||
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||||||
@ -1,41 +0,0 @@
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|||||||
version: '2.1'
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|
||||||
|
|
||||||
services:
|
|
||||||
jenkins-master:
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|
||||||
image: jenkinsci/blueocean:latest
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|
||||||
ports:
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|
||||||
- 8080
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|
||||||
- 50000
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|
||||||
volumes:
|
|
||||||
- molgenis-jenkins:/var/jenkins_home
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|
||||||
restart: always
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|
||||||
labels:
|
|
||||||
io.rancher.container.pull_image: always
|
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
|
||||||
traefik.enable: true
|
|
||||||
traefik.port: 8080
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|
||||||
healthcheck:
|
|
||||||
test: ["CMD", "curl", "-sS", "http://localhost:50000" ]
|
|
||||||
interval: 5s
|
|
||||||
timeout: 10s
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|
||||||
retries: 5
|
|
||||||
|
|
||||||
jenkins-agent-maven:
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|
||||||
image: registry.molgenis.org/docker-molgenis-ops-releases/jenkins-agent-buildtools:lts
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|
||||||
environment:
|
|
||||||
- JENKINS_URL=http://localhost:8080
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|
||||||
- JENKINS_SECRET=paradoxa
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|
||||||
- JENKINS_AGENT_NAME=buildtools
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|
||||||
volumes:
|
|
||||||
- molgenis-jenkins-agent-buildtools:/var/jenkins_home
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|
||||||
depends_on:
|
|
||||||
jenkins-master:
|
|
||||||
condition: service_healthy
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|
||||||
restart: always
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|
||||||
|
|
||||||
volumes:
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|
||||||
molgenis-jenkins:
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|
||||||
driver: rancher-nfs
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|
||||||
molgenis-jenkins-agent-buildtools:
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|
||||||
driver: rancher-nfs
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|
||||||
@ -1,18 +0,0 @@
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|||||||
.catalog:
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|
||||||
name: jenkins
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|
||||||
version: latest
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|
||||||
description: Jenkins for Molgenis
|
|
||||||
minimum_rancher_version: v1.6.3
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|
||||||
questions:
|
|
||||||
- variable: "DOMAINS"
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|
||||||
description: "Domain you want to use (comma seperated)"
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|
||||||
label: "Domains:"
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|
||||||
required: true
|
|
||||||
default: "test.molgenis.org,test.dcktest.gcc.rug.nl"
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|
||||||
type: "string"
|
|
||||||
- variable: "TRAEFIK_BACKEND"
|
|
||||||
description: "Name of the server when added to loadbalancer"
|
|
||||||
label: "Traefik backend:"
|
|
||||||
required: true
|
|
||||||
default: "test.molgenis.org"
|
|
||||||
type: "string"
|
|
||||||
File diff suppressed because it is too large
Load Diff
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@ -1,7 +0,0 @@
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|||||||
name: Jenkins
|
|
||||||
description: |
|
|
||||||
Jenkins for Molgenis
|
|
||||||
version: v1.0.0
|
|
||||||
category: All
|
|
||||||
maintainer: Molgenis DEVOPS-team
|
|
||||||
projectURL: https://jenkins.io
|
|
||||||
@ -1,21 +1,17 @@
|
|||||||
# MOLGENIS
|
# 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:
|
||||||
These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
|
|
||||||
|
|
||||||
- MOLGENIS
|
- MOLGENIS instance
|
||||||
- MOLGENIS-OpenCPU
|
- Postgress instance
|
||||||
- Postgress
|
- ElasticSearch instance
|
||||||
- ElasticSearch
|
|
||||||
|
## Usage:
|
||||||
|
|
||||||
## Usage
|
|
||||||
- Select MOLGENIS from catalog
|
- Select MOLGENIS from catalog
|
||||||
- Fill in the questions in the template area
|
- Enter the name of the replica set
|
||||||
- Click *Launch*
|
- Click deploy
|
||||||
|
|
||||||
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.
|
||||||
@ -1,82 +1,22 @@
|
|||||||
version: '2'
|
app:
|
||||||
|
image: sidohaakma/molgenis-docker:2.0.0
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.molgenis.org/molgenis/molgenis:latest
|
|
||||||
ports:
|
ports:
|
||||||
- 8080
|
- 8081:8080
|
||||||
links:
|
links:
|
||||||
- postgres
|
- db
|
||||||
- elasticsearch
|
|
||||||
volumes:
|
volumes:
|
||||||
- molgenis-data:/opt/molgenis
|
- app-data:/opt/molgenis
|
||||||
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}"
|
|
||||||
- "molgenis.home=/opt/molgenis"
|
|
||||||
- "admin.password=${MOLGENIS_ADMIN_PASSWORD}"
|
|
||||||
- "opencpu.uri.port=8004"
|
|
||||||
- "elasticsearch.cluster.name=${ELASTIC_CLUSTER}"
|
|
||||||
- "elasticsearch.transport.addresses=elasticsearch:9300"
|
|
||||||
- "JAVA_OPTS=-Xmx${JVM_MEM_POOL} -Xms${JVM_MEM_POOL} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
|
||||||
labels:
|
labels:
|
||||||
io.rancher.container.pull_image: always
|
io.rancher.container.create_agent: 'true'
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
io.rancher.scheduler.global: 'true'
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
db:
|
||||||
traefik.enable: true
|
build: ./db
|
||||||
traefik.port: 8080
|
expose:
|
||||||
|
|
||||||
postgres:
|
|
||||||
image: postgres:9.6-alpine
|
|
||||||
environment:
|
|
||||||
- POSTGRES_USER=${DB_USERNAME}
|
|
||||||
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
|
||||||
- POSTGRES_DB=${DB_SCHEME}
|
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
ports:
|
|
||||||
- 5432
|
- 5432
|
||||||
healthcheck:
|
|
||||||
test: ["CMD", "curl", "sS", "http://localhost:8080"]
|
|
||||||
interval: 5s
|
|
||||||
timeout: 10s
|
|
||||||
retries: 5
|
|
||||||
|
|
||||||
opencpu:
|
|
||||||
image: registry.molgenis.org/molgenis/molgenis-opencpu:latest
|
|
||||||
ports:
|
|
||||||
- 8004
|
|
||||||
healthcheck:
|
|
||||||
test: ["CMD", "curl", "sS", "http://localhost:8084"]
|
|
||||||
interval: 5s
|
|
||||||
timeout: 10s
|
|
||||||
retries: 5
|
|
||||||
|
|
||||||
elasticsearch:
|
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
|
||||||
environment:
|
|
||||||
- "cluster.name=${ELASTIC_CLUSTER}"
|
|
||||||
- "bootstrap.memory_lock=true"
|
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
|
||||||
- "xpack.security.enabled=false"
|
|
||||||
ulimits:
|
|
||||||
memlock:
|
|
||||||
soft: -1
|
|
||||||
hard: -1
|
|
||||||
ports:
|
|
||||||
- 9200
|
|
||||||
- 9300
|
|
||||||
volumes:
|
volumes:
|
||||||
- elastic-data
|
- db-data:/var/lib/postgresql/data
|
||||||
|
labels:
|
||||||
|
io.rancher.container.create_agent: 'true'
|
||||||
volumes:
|
volumes:
|
||||||
postgres-data:
|
db-data:
|
||||||
driver: local
|
app-data:
|
||||||
molgenis-data:
|
|
||||||
driver: local
|
|
||||||
elastic-data:
|
|
||||||
driver: local
|
|
||||||
|
|
||||||
|
|||||||
@ -1,54 +1,5 @@
|
|||||||
.catalog:
|
.catalog:
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: latest
|
version: v2.0.0
|
||||||
description: Molgenis
|
description: Molgenis
|
||||||
minimum_rancher_version: v1.6.3
|
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: "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"
|
|
||||||
- variable: "JVM_MEM_POOL"
|
|
||||||
description: "Specifies the initial and maximum size, in bytes, of the memory allocation pool."
|
|
||||||
label: "Initial and maximum size:"
|
|
||||||
required: true
|
|
||||||
default: "2g"
|
|
||||||
type: "string"
|
|
||||||
@ -1,21 +1,18 @@
|
|||||||
# MOLGENIS
|
# MOLGENIS
|
||||||
Flexible software for scientific data
|
**Flexible software for scientific data**
|
||||||
|
|
||||||
## Rancher configuration
|
|
||||||
These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
|
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
|
||||||
|
|
||||||
- MOLGENIS
|
- MOLGENIS
|
||||||
- MOLGENIS-OpenCPU
|
- Elasticsearch is packaged with MOLGENIS
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
|
||||||
|
|
||||||
## Usage
|
**Usage:**
|
||||||
|
|
||||||
|
|
||||||
- Select MOLGENIS from catalog
|
- Select MOLGENIS from catalog
|
||||||
- Fill in the questions in the template area
|
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
|
||||||
- Click *Launch*
|
- Click *Launch*
|
||||||
|
|
||||||
MOLGENIS can now be accessed over the Rancher network on the domains you specified.
|
MOLGENIS can now be accessed over the Rancher network.
|
||||||
|
|
||||||
## Loadbalancers
|
|
||||||
You can check lb.molgenis.org to check the availabity of the stack.
|
|
||||||
|
|
||||||
@ -1,69 +1,45 @@
|
|||||||
version: '2'
|
app:
|
||||||
|
image: sidohaakma/molgenis-docker:4.1.0
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:stable
|
|
||||||
ports:
|
ports:
|
||||||
- 8080
|
- 8081:8080
|
||||||
links:
|
links:
|
||||||
- postgres
|
- db
|
||||||
- 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.container.pull_image: always
|
io.rancher.sidekicks: molgenis-data
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
io.rancher.scheduler.global: true
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
traefik.enable: true
|
io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
traefik.port: 8080
|
db:
|
||||||
|
|
||||||
postgres:
|
|
||||||
image: postgres:9.6-alpine
|
image: postgres:9.6-alpine
|
||||||
environment:
|
environment:
|
||||||
- POSTGRES_USER=${DB_USERNAME}
|
- POSTGRES_USER=molgenis
|
||||||
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
- POSTGRES_PASSWORD=molgenis
|
||||||
- POSTGRES_DB=${DB_SCHEME}
|
- POSTGRES_DB=molgenis
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
expose:
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
ports:
|
|
||||||
- 5432
|
- 5432
|
||||||
|
volumes_from:
|
||||||
|
- postgres-data
|
||||||
|
labels:
|
||||||
|
io.rancher.sidekicks: postgres-data
|
||||||
|
io.rancher.scheduler.global: true
|
||||||
|
io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
|
io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
|
|
||||||
opencpu:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable
|
|
||||||
ports:
|
|
||||||
- 8004
|
|
||||||
|
|
||||||
elasticsearch:
|
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
|
||||||
environment:
|
|
||||||
- "cluster.name=${ELASTIC_CLUSTER}"
|
|
||||||
- "bootstrap.memory_lock=true"
|
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
|
||||||
- "xpack.security.enabled=false"
|
|
||||||
ulimits:
|
|
||||||
memlock:
|
|
||||||
soft: -1
|
|
||||||
hard: -1
|
|
||||||
ports:
|
|
||||||
- 9200
|
|
||||||
- 9300
|
|
||||||
volumes:
|
|
||||||
- elastic-data
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
postgres-data:
|
postgres-data:
|
||||||
driver: local
|
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:
|
||||||
|
- /var/lib/postgresql/data/pgdata
|
||||||
molgenis-data:
|
molgenis-data:
|
||||||
driver: local
|
image: busybox
|
||||||
elastic-data:
|
labels:
|
||||||
driver: local
|
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:
|
||||||
|
- /opt/molgenis
|
||||||
@ -1,58 +1,5 @@
|
|||||||
.catalog:
|
.catalog:
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: stable
|
version: v4.1.0
|
||||||
description: Molgenis
|
description: Molgenis
|
||||||
minimum_rancher_version: v1.6.3
|
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: "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
|
|
||||||
health_check:
|
|
||||||
port: 8080
|
|
||||||
interval: 5000
|
|
||||||
unhealthy_threshold: 3
|
|
||||||
request_line: 'GET / HTTP/1.0'
|
|
||||||
healthy_threshold: 2
|
|
||||||
response_timeout: 5000
|
|
||||||
|
|||||||
@ -1,21 +1,18 @@
|
|||||||
# MOLGENIS
|
# MOLGENIS
|
||||||
Flexible software for scientific data
|
**Flexible software for scientific data**
|
||||||
|
|
||||||
## Rancher configuration
|
|
||||||
These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
|
This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services:
|
||||||
|
|
||||||
- MOLGENIS
|
- MOLGENIS
|
||||||
- MOLGENIS-OpenCPU
|
|
||||||
- Postgress
|
- Postgress
|
||||||
- ElasticSearch
|
- ElasticSearch
|
||||||
|
|
||||||
## Usage
|
**Usage:**
|
||||||
|
|
||||||
|
|
||||||
- Select MOLGENIS from catalog
|
- Select MOLGENIS from catalog
|
||||||
- Fill in the questions in the template area
|
- The stack-name must not be altered (this is hardcoded in de docker-compose file)
|
||||||
- Click *Launch*
|
- Click *Launch*
|
||||||
|
|
||||||
MOLGENIS can now be accessed over the Rancher network on the domains you specified.
|
MOLGENIS can now be accessed over the Rancher network.
|
||||||
|
|
||||||
## Loadbalancers
|
|
||||||
You can check lb.molgenis.org to check the availabity of the stack.
|
|
||||||
|
|
||||||
@ -1,27 +1,85 @@
|
|||||||
services:
|
|
||||||
molgenis:
|
molgenis:
|
||||||
image: registry.webhosting.rug.nl/molgenis:2.0.1
|
image: sidohaakma/molgenis-docker:5.2.0
|
||||||
ports:
|
ports:
|
||||||
- 8080
|
- 8081:8080
|
||||||
links:
|
links:
|
||||||
- db
|
- postgres
|
||||||
volumes:
|
- elasticsearch
|
||||||
- molgenis-data:/opt/molgenis
|
volumes_from:
|
||||||
|
- molgenis-data
|
||||||
labels:
|
labels:
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
io.rancher.sidekicks: molgenis-data
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
io.rancher.scheduler.global: true
|
||||||
traefik.enable: true
|
io.rancher.container.pull_image: always
|
||||||
traefik.port: 8080
|
io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
|
io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
postgres:
|
postgres:
|
||||||
image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1
|
image: postgres:9.6-alpine
|
||||||
expose:
|
environment:
|
||||||
|
- POSTGRES_USER=molgenis
|
||||||
|
- POSTGRES_PASSWORD=molgenis
|
||||||
|
- POSTGRES_DB=molgenis
|
||||||
|
- PGDATA=/var/lib/postgresql/data/pgdata
|
||||||
|
volumes_from:
|
||||||
|
- postgres-data
|
||||||
|
ports:
|
||||||
- 5432
|
- 5432
|
||||||
volumes:
|
labels:
|
||||||
- postgres-data:/var/lib/postgresql/data
|
io.rancher.sidekicks: postgres-data
|
||||||
|
io.rancher.scheduler.global: true
|
||||||
|
io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
|
io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
|
elasticsearch:
|
||||||
|
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
||||||
|
environment:
|
||||||
|
- "cluster.name=molgenis"
|
||||||
|
- "bootstrap.memory_lock=true"
|
||||||
|
- "ES_JAVA_OPTS=-Xms512m -Xmx512m"
|
||||||
|
- "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
|
||||||
|
io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
|
io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
|
# loadbalancer:
|
||||||
|
# image: rancher/lb-service-haproxy:v0.7.5
|
||||||
|
# ports:
|
||||||
|
# - 80
|
||||||
|
# labels:
|
||||||
|
# io.rancher.scheduler.global: true
|
||||||
|
# io.rancher.scheduler.affinity:host_label: type=molgenis
|
||||||
|
# io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis
|
||||||
|
|
||||||
volumes:
|
|
||||||
postgres-data:
|
postgres-data:
|
||||||
driver: local
|
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:
|
||||||
|
- /var/lib/postgresql/data/pgdata
|
||||||
molgenis-data:
|
molgenis-data:
|
||||||
driver: local
|
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:
|
||||||
|
- /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
|
||||||
|
|||||||
@ -1,28 +1,18 @@
|
|||||||
.catalog:
|
.catalog:
|
||||||
name: molgenis
|
name: molgenis
|
||||||
version: v2.0.0
|
version: v5.0.0
|
||||||
description: Molgenis
|
description: Molgenis
|
||||||
minimum_rancher_version: v1.6.3
|
minimum_rancher_version: v1.6.3
|
||||||
questions:
|
#loadbalancer:
|
||||||
- variable: "DOMAINS"
|
# scale: 1
|
||||||
description: "Domain you want to use (comma seperated)"
|
# lb_config:
|
||||||
label: "Domains:"
|
# port_rules:
|
||||||
required: true
|
# - source_port: 80
|
||||||
default: "test.molgenis.org,test.dcktest.gcc.rug.nl"
|
# target_port: 8081
|
||||||
type: "string"
|
# service: molgenis
|
||||||
- variable: "TRAEFIK_BACKEND"
|
# health_check:
|
||||||
description: "Name of the server when added to loadbalancer"
|
# port: 42
|
||||||
label: "Traefik backend:"
|
# interval: 2000
|
||||||
required: true
|
# unhealthy_threshold: 3
|
||||||
default: "test.molgenis.org"
|
# healthy_threshold: 2
|
||||||
type: "string"
|
# response_timeout: 2000
|
||||||
|
|
||||||
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
|
|
||||||
@ -1,17 +0,0 @@
|
|||||||
# 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
|
|
||||||
|
|
||||||
## 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.
|
|
||||||
@ -1,32 +0,0 @@
|
|||||||
version: '2'
|
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0
|
|
||||||
ports:
|
|
||||||
- 8080
|
|
||||||
links:
|
|
||||||
- postgres
|
|
||||||
volumes:
|
|
||||||
- molgenis-data
|
|
||||||
labels:
|
|
||||||
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
|
|
||||||
expose:
|
|
||||||
- 5432
|
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
molgenis-data:
|
|
||||||
driver: local
|
|
||||||
postgres-data:
|
|
||||||
driver: local
|
|
||||||
@ -1,28 +0,0 @@
|
|||||||
.catalog:
|
|
||||||
name: molgenis
|
|
||||||
version: v4.1.0
|
|
||||||
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: "Traefik 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
|
|
||||||
@ -1,21 +0,0 @@
|
|||||||
# MOLGENIS
|
|
||||||
Flexible software for scientific data
|
|
||||||
|
|
||||||
## 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
|
|
||||||
- MOLGENIS-OpenCPU
|
|
||||||
- Postgress
|
|
||||||
- ElasticSearch
|
|
||||||
|
|
||||||
## Usage
|
|
||||||
- Select MOLGENIS from catalog
|
|
||||||
- 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.
|
|
||||||
|
|
||||||
@ -1,68 +0,0 @@
|
|||||||
version: '2'
|
|
||||||
|
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
|
|
||||||
ports:
|
|
||||||
- 8080
|
|
||||||
links:
|
|
||||||
- postgres
|
|
||||||
- elasticsearch
|
|
||||||
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.container.pull_image: always
|
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
|
||||||
traefik.enable: true
|
|
||||||
traefik.port: 8080
|
|
||||||
|
|
||||||
postgres:
|
|
||||||
image: postgres:9.6-alpine
|
|
||||||
environment:
|
|
||||||
- POSTGRES_USER=${DB_USERNAME}
|
|
||||||
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
|
||||||
- POSTGRES_DB=${DB_SCHEME}
|
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
ports:
|
|
||||||
- 5432
|
|
||||||
|
|
||||||
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=${ELASTIC_CLUSTER}"
|
|
||||||
- "bootstrap.memory_lock=true"
|
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
|
||||||
- "xpack.security.enabled=false"
|
|
||||||
ulimits:
|
|
||||||
memlock:
|
|
||||||
soft: -1
|
|
||||||
hard: -1
|
|
||||||
ports:
|
|
||||||
- 9200
|
|
||||||
- 9300
|
|
||||||
volumes:
|
|
||||||
- elastic-data
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
postgres-data:
|
|
||||||
driver: local
|
|
||||||
molgenis-data:
|
|
||||||
driver: local
|
|
||||||
elastic-data:
|
|
||||||
driver: local
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
.catalog:
|
|
||||||
name: molgenis
|
|
||||||
version: v5.2.0
|
|
||||||
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: "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
|
|
||||||
health_check:
|
|
||||||
port: 8080
|
|
||||||
interval: 5000
|
|
||||||
unhealthy_threshold: 3
|
|
||||||
request_line: 'GET / HTTP/1.0'
|
|
||||||
healthy_threshold: 2
|
|
||||||
response_timeout: 5000
|
|
||||||
@ -1,21 +0,0 @@
|
|||||||
# MOLGENIS
|
|
||||||
Flexible software for scientific data
|
|
||||||
|
|
||||||
## 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
|
|
||||||
- MOLGENIS-OpenCPU
|
|
||||||
- Postgress
|
|
||||||
- ElasticSearch
|
|
||||||
|
|
||||||
## Usage
|
|
||||||
- Select MOLGENIS from catalog
|
|
||||||
- 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.
|
|
||||||
|
|
||||||
@ -1,68 +0,0 @@
|
|||||||
version: '2'
|
|
||||||
|
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
|
|
||||||
ports:
|
|
||||||
- 8080
|
|
||||||
links:
|
|
||||||
- postgres
|
|
||||||
- elasticsearch
|
|
||||||
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.container.pull_image: always
|
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
|
||||||
traefik.enable: true
|
|
||||||
traefik.port: 8080
|
|
||||||
|
|
||||||
postgres:
|
|
||||||
image: postgres:9.6-alpine
|
|
||||||
environment:
|
|
||||||
- POSTGRES_USER=${DB_USERNAME}
|
|
||||||
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
|
||||||
- POSTGRES_DB=${DB_SCHEME}
|
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
ports:
|
|
||||||
- 5432
|
|
||||||
|
|
||||||
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=${ELASTIC_CLUSTER}"
|
|
||||||
- "bootstrap.memory_lock=true"
|
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
|
||||||
- "xpack.security.enabled=false"
|
|
||||||
ulimits:
|
|
||||||
memlock:
|
|
||||||
soft: -1
|
|
||||||
hard: -1
|
|
||||||
ports:
|
|
||||||
- 9200
|
|
||||||
- 9300
|
|
||||||
volumes:
|
|
||||||
- elastic-data
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
postgres-data:
|
|
||||||
driver: local
|
|
||||||
molgenis-data:
|
|
||||||
driver: local
|
|
||||||
elastic-data:
|
|
||||||
driver: local
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
.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: "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
|
|
||||||
health_check:
|
|
||||||
port: 8080
|
|
||||||
interval: 5000
|
|
||||||
unhealthy_threshold: 3
|
|
||||||
request_line: 'GET / HTTP/1.0'
|
|
||||||
healthy_threshold: 2
|
|
||||||
response_timeout: 5000
|
|
||||||
@ -1,21 +0,0 @@
|
|||||||
# MOLGENIS
|
|
||||||
Flexible software for scientific data
|
|
||||||
|
|
||||||
## 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
|
|
||||||
- MOLGENIS-OpenCPU
|
|
||||||
- Postgress
|
|
||||||
- ElasticSearch
|
|
||||||
|
|
||||||
## Usage
|
|
||||||
- Select MOLGENIS from catalog
|
|
||||||
- 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.
|
|
||||||
|
|
||||||
@ -1,68 +0,0 @@
|
|||||||
version: '2'
|
|
||||||
|
|
||||||
services:
|
|
||||||
molgenis:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0
|
|
||||||
ports:
|
|
||||||
- 8080
|
|
||||||
links:
|
|
||||||
- postgres
|
|
||||||
- elasticsearch
|
|
||||||
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.container.pull_image: always
|
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
|
||||||
traefik.enable: true
|
|
||||||
traefik.port: 8080
|
|
||||||
|
|
||||||
postgres:
|
|
||||||
image: postgres:9.6-alpine
|
|
||||||
environment:
|
|
||||||
- POSTGRES_USER=${DB_USERNAME}
|
|
||||||
- POSTGRES_PASSWORD=${DB_PASSWORD}
|
|
||||||
- POSTGRES_DB=${DB_SCHEME}
|
|
||||||
- PGDATA=/var/lib/postgresql/data/pgdata
|
|
||||||
volumes:
|
|
||||||
- postgres-data
|
|
||||||
ports:
|
|
||||||
- 5432
|
|
||||||
|
|
||||||
opencpu:
|
|
||||||
image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:7.0.0
|
|
||||||
ports:
|
|
||||||
- 8004
|
|
||||||
|
|
||||||
elasticsearch:
|
|
||||||
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1
|
|
||||||
environment:
|
|
||||||
- "cluster.name=${ELASTIC_CLUSTER}"
|
|
||||||
- "bootstrap.memory_lock=true"
|
|
||||||
- "ES_JAVA_OPTS=-Xms1g -Xmx1g"
|
|
||||||
- "xpack.security.enabled=false"
|
|
||||||
ulimits:
|
|
||||||
memlock:
|
|
||||||
soft: -1
|
|
||||||
hard: -1
|
|
||||||
ports:
|
|
||||||
- 9200
|
|
||||||
- 9300
|
|
||||||
volumes:
|
|
||||||
- elastic-data
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
postgres-data:
|
|
||||||
driver: local
|
|
||||||
molgenis-data:
|
|
||||||
driver: local
|
|
||||||
elastic-data:
|
|
||||||
driver: local
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
.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: "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
|
|
||||||
health_check:
|
|
||||||
port: 8080
|
|
||||||
interval: 5000
|
|
||||||
unhealthy_threshold: 3
|
|
||||||
request_line: 'GET / HTTP/1.0'
|
|
||||||
healthy_threshold: 2
|
|
||||||
response_timeout: 5000
|
|
||||||
@ -1,7 +1,7 @@
|
|||||||
name: Molgenis
|
name: Molgenis
|
||||||
description: |
|
description: |
|
||||||
Molgenis | Flexible software for scientific data
|
Molgenis | Flexible software for scientific data
|
||||||
version: latest
|
version: v5.0.0
|
||||||
category: All
|
category: All
|
||||||
maintainer: Molgenis DEV-team and community-members
|
maintainer: Molgenis DEV-team and community-members
|
||||||
projectURL: https://www.molgenis.org
|
projectURL: http://molgenis.org
|
||||||
@ -1,16 +0,0 @@
|
|||||||
# Nexus for MOLGENIS
|
|
||||||
Flexible software for scientific data
|
|
||||||
|
|
||||||
## Rancher configuration
|
|
||||||
These templates can create a range of MOLGENIS stacks on top of Rancher. The latests and stable release serves 4 docker services:
|
|
||||||
|
|
||||||
- Nexus
|
|
||||||
|
|
||||||
## Usage
|
|
||||||
- Select Nexus from catalog
|
|
||||||
- Fill in the questions in the template area
|
|
||||||
- Click *Launch*
|
|
||||||
|
|
||||||
## Loadbalancers
|
|
||||||
You can check lb.molgenis.org to check the availability of the stack.
|
|
||||||
|
|
||||||
@ -1,20 +0,0 @@
|
|||||||
version: '2'
|
|
||||||
|
|
||||||
services:
|
|
||||||
nexus:
|
|
||||||
image: sonatype/nexus3:latest
|
|
||||||
ports:
|
|
||||||
- 8081
|
|
||||||
- 5000
|
|
||||||
volumes:
|
|
||||||
- molgenis-nexus-data:/nexus-data
|
|
||||||
labels:
|
|
||||||
io.rancher.container.pull_image: always
|
|
||||||
traefik.frontend.rule: Host:${DOMAINS}
|
|
||||||
traefik.backend: ${TRAEFIK_BACKEND}
|
|
||||||
traefik.enable: true
|
|
||||||
traefik.port: 8081
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
molgenis-nexus-data:
|
|
||||||
driver: rancher-nfs
|
|
||||||
@ -1,28 +0,0 @@
|
|||||||
.catalog:
|
|
||||||
name: nexus
|
|
||||||
version: latest
|
|
||||||
description: Nexus for 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: "Traefik 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
|
|
||||||
@ -1,551 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
|
||||||
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
|
|
||||||
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|
|
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7wAAAABJRU5ErkJggg==" />
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||||||
</svg>
|
|
||||||
|
Before Width: | Height: | Size: 42 KiB |
@ -1,7 +0,0 @@
|
|||||||
name: Nexus
|
|
||||||
description: |
|
|
||||||
Nexus for Molgenis
|
|
||||||
version: v1.0.0
|
|
||||||
category: All
|
|
||||||
maintainer: Molgenis DEVOPS-team
|
|
||||||
projectURL: https://www.sonatype.com/nexus-repository-oss
|
|
||||||
Loading…
Reference in New Issue
Block a user