From f832f9806ee4e5b8b9dd1430200566ee5fd42bc2 Mon Sep 17 00:00:00 2001 From: sido Date: Thu, 15 Mar 2018 00:20:13 +0100 Subject: [PATCH 1/3] chore(0 and 1): added latest and stable tag --- templates/molgenis/0/README.md | 17 ++-- templates/molgenis/0/docker-compose.yml | 106 ++++++++++++++++++----- templates/molgenis/0/rancher-compose.yml | 4 +- templates/molgenis/1/README.md | 5 +- templates/molgenis/1/docker-compose.yml | 85 +++++++++++++----- templates/molgenis/1/rancher-compose.yml | 4 +- templates/molgenis/2/README.md | 17 ++-- templates/molgenis/2/docker-compose.yml | 100 +++++---------------- templates/molgenis/2/rancher-compose.yml | 2 +- templates/molgenis/3/README.md | 5 +- templates/molgenis/3/docker-compose.yml | 78 +++++------------ templates/molgenis/3/rancher-compose.yml | 4 +- templates/molgenis/4/docker-compose.yml | 24 ++--- templates/molgenis/4/rancher-compose.yml | 4 +- templates/molgenis/5/README.md | 16 ++++ templates/molgenis/5/docker-compose.yml | 78 +++++++++++++++++ templates/molgenis/5/rancher-compose.yml | 28 ++++++ templates/molgenis/6/README.md | 16 ++++ templates/molgenis/6/docker-compose.yml | 85 ++++++++++++++++++ templates/molgenis/6/rancher-compose.yml | 28 ++++++ 20 files changed, 482 insertions(+), 224 deletions(-) create mode 100644 templates/molgenis/5/README.md create mode 100644 templates/molgenis/5/docker-compose.yml create mode 100644 templates/molgenis/5/rancher-compose.yml create mode 100644 templates/molgenis/6/README.md create mode 100644 templates/molgenis/6/docker-compose.yml create mode 100644 templates/molgenis/6/rancher-compose.yml diff --git a/templates/molgenis/0/README.md b/templates/molgenis/0/README.md index 6550a69..b65dd55 100644 --- a/templates/molgenis/0/README.md +++ b/templates/molgenis/0/README.md @@ -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. \ No newline at end of file diff --git a/templates/molgenis/0/docker-compose.yml b/templates/molgenis/0/docker-compose.yml index a5e1808..5f8871e 100644 --- a/templates/molgenis/0/docker-compose.yml +++ b/templates/molgenis/0/docker-compose.yml @@ -1,21 +1,85 @@ -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: ${TRAEFIK_BACKEND} - traefik.enable: true - traefik.port: 8080 -db: - image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1 - expose: - - 5432 - volumes: - - db-data:/var/lib/postgresql/data + molgenis: + image: registry.webhosting.rug.nl/molgenis/molgenis:stable + ports: + - 8080 + links: + - postgres + - elasticsearch + volumes_from: + - molgenis-data + environment: + - "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE" + - "db_driver=org.postgresql.Driver" + - "db_user=molgenis" + - "db_password=molgenis" + - "elasticsearch.cluster.name=molgenis" + - "elasticsearch.transport.addresses=elasticsearch:9300" + labels: + io.rancher.sidekicks: molgenis-data + io.rancher.container.pull_image: always + io.rancher.scheduler.global: true + traefik.frontend.rule: Host:${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: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: + - /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 diff --git a/templates/molgenis/0/rancher-compose.yml b/templates/molgenis/0/rancher-compose.yml index 99aa579..7892b93 100644 --- a/templates/molgenis/0/rancher-compose.yml +++ b/templates/molgenis/0/rancher-compose.yml @@ -1,6 +1,6 @@ .catalog: name: molgenis - version: v2.0.0 + version: latest description: Molgenis minimum_rancher_version: v1.6.3 questions: @@ -25,4 +25,4 @@ unhealthy_threshold: 3 request_line: 'GET / HTTP/1.0' healthy_threshold: 2 - response_timeout: 5000 \ No newline at end of file + response_timeout: 5000 diff --git a/templates/molgenis/1/README.md b/templates/molgenis/1/README.md index 36bc32f..b65dd55 100644 --- a/templates/molgenis/1/README.md +++ b/templates/molgenis/1/README.md @@ -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 +- MOLGENIS - Postgress +- ElasticSearch ## Usage - Select MOLGENIS from catalog diff --git a/templates/molgenis/1/docker-compose.yml b/templates/molgenis/1/docker-compose.yml index 181d839..601cc58 100644 --- a/templates/molgenis/1/docker-compose.yml +++ b/templates/molgenis/1/docker-compose.yml @@ -1,42 +1,85 @@ -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: ${TRAEFIK_BACKEND} - traefik.enable: true - traefik.port: 8080 + molgenis: + image: registry.webhosting.rug.nl/molgenis/molgenis:latest + ports: + - 8080 + links: + - postgres + - elasticsearch + volumes_from: + - molgenis-data + environment: + - "db_uri=jdbc:postgresql://postgres/molgenis?reWriteBatchedInserts=true&autosave=CONSERVATIVE" + - "db_driver=org.postgresql.Driver" + - "db_user=molgenis" + - "db_password=molgenis" + - "elasticsearch.cluster.name=molgenis" + - "elasticsearch.transport.addresses=elasticsearch:9300" + labels: + io.rancher.sidekicks: molgenis-data + io.rancher.container.pull_image: always + io.rancher.scheduler.global: true + traefik.frontend.rule: Host:${DOMAINS} + traefik.backend: ${TRAEFIK_BACKEND} + traefik.enable: true + traefik.port: 8080 - db: + postgres: image: postgres:9.6-alpine environment: - POSTGRES_USER=molgenis - POSTGRES_PASSWORD=molgenis - POSTGRES_DB=molgenis - expose: - - 5432 - volumes_from: + - PGDATA=/var/lib/postgresql/data/pgdata + volumes_from: - postgres-data + ports: + - 5432 labels: io.rancher.sidekicks: postgres-data io.rancher.scheduler.global: true - postgres-data: + 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 \ No newline at end of file + - /opt/molgenis + +# elasticsearch-data: +# image: busybox +# labels: +# io.rancher.container.start_once: true +# volumes: +# - /usr/share/elasticsearch/data diff --git a/templates/molgenis/1/rancher-compose.yml b/templates/molgenis/1/rancher-compose.yml index 101efaf..e05cdbf 100644 --- a/templates/molgenis/1/rancher-compose.yml +++ b/templates/molgenis/1/rancher-compose.yml @@ -1,6 +1,6 @@ .catalog: name: molgenis - version: v4.1.0 + version: stable description: Molgenis minimum_rancher_version: v1.6.3 questions: @@ -25,4 +25,4 @@ unhealthy_threshold: 3 request_line: 'GET / HTTP/1.0' healthy_threshold: 2 - response_timeout: 5000 \ No newline at end of file + response_timeout: 5000 diff --git a/templates/molgenis/2/README.md b/templates/molgenis/2/README.md index b65dd55..6550a69 100644 --- a/templates/molgenis/2/README.md +++ b/templates/molgenis/2/README.md @@ -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. \ No newline at end of file diff --git a/templates/molgenis/2/docker-compose.yml b/templates/molgenis/2/docker-compose.yml index 43309fa..a5e1808 100644 --- a/templates/molgenis/2/docker-compose.yml +++ b/templates/molgenis/2/docker-compose.yml @@ -1,79 +1,21 @@ - molgenis: - image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0 - 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: ${TRAEFIK_BACKEND} - traefik.enable: true - traefik.port: 8080 - - postgres: - image: postgres:9.6-alpine - environment: - - POSTGRES_USER=molgenis - - POSTGRES_PASSWORD=molgenis - - POSTGRES_DB=molgenis - - PGDATA=/var/lib/postgresql/data/pgdata - volumes_from: - - postgres-data - ports: - - 5432 - labels: - io.rancher.sidekicks: postgres-data - io.rancher.scheduler.global: true - - elasticsearch: - image: docker.elastic.co/elasticsearch/elasticsearch:5.5.1 - environment: - - "cluster.name=molgenis" - - "bootstrap.memory_lock=true" - - "ES_JAVA_OPTS=-Xms1g -Xmx1g" - - "xpack.security.enabled=false" - ulimits: - memlock: - soft: -1 - hard: -1 -# volumes_from: -# - elasticsearch-data - ports: - - 9200:9200 - - 9300:9300 -# labels: - #io.rancher.sidekicks: elasticsearch-data - - opencpu: - image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:5.2.0 - ports: - - 8004:8004 - - postgres-data: - image: busybox - labels: - io.rancher.container.start_once: true - volumes: - - /var/lib/postgresql/data/pgdata - - molgenis-data: - image: busybox - labels: - io.rancher.container.start_once: true - volumes: - - /opt/molgenis - -# elasticsearch-data: -# image: busybox -# labels: -# io.rancher.container.start_once: true -# io.rancher.scheduler.affinity:host_label: type=molgenis -# io.rancher.scheduler.affinity:container_label: io.rancher.stack.name=molgenis -# volumes: -# - /usr/share/elasticsearch/data +app: + image: registry.webhosting.rug.nl/molgenis:2.0.1 + ports: + - 8081:8080 + links: + - db + volumes: + - app-data:/opt/molgenis + labels: + io.rancher.container.create_agent: true + io.rancher.scheduler.global: true + traefik.frontend.rule: Host:${DOMAINS} + traefik.backend: ${TRAEFIK_BACKEND} + traefik.enable: true + traefik.port: 8080 +db: + image: registry.webhosting.rug.nl/molgenis-postgres:2.0.1 + expose: + - 5432 + volumes: + - db-data:/var/lib/postgresql/data diff --git a/templates/molgenis/2/rancher-compose.yml b/templates/molgenis/2/rancher-compose.yml index a42daa3..99aa579 100644 --- a/templates/molgenis/2/rancher-compose.yml +++ b/templates/molgenis/2/rancher-compose.yml @@ -1,6 +1,6 @@ .catalog: name: molgenis - version: v5.2.0 + version: v2.0.0 description: Molgenis minimum_rancher_version: v1.6.3 questions: diff --git a/templates/molgenis/3/README.md b/templates/molgenis/3/README.md index b65dd55..36bc32f 100644 --- a/templates/molgenis/3/README.md +++ b/templates/molgenis/3/README.md @@ -1,12 +1,13 @@ # MOLGENIS + Flexible software for scientific data ## Rancher configuration This template creates a MOLGENIS stack on top of Rancher. It creates 3 docker services: -- MOLGENIS +- MOLGENIS + - Elasticsearch is packaged with MOLGENIS - Postgress -- ElasticSearch ## Usage - Select MOLGENIS from catalog diff --git a/templates/molgenis/3/docker-compose.yml b/templates/molgenis/3/docker-compose.yml index da54e3d..181d839 100644 --- a/templates/molgenis/3/docker-compose.yml +++ b/templates/molgenis/3/docker-compose.yml @@ -1,78 +1,42 @@ - molgenis: - image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0 - ports: - - 8080 - links: - - postgres - - elasticsearch - volumes_from: - - molgenis-data - labels: - io.rancher.sidekicks: molgenis-data - io.rancher.container.pull_image: always - io.rancher.scheduler.global: true - traefik.frontend.rule: Host:${DOMAINS} - traefik.backend: ${TRAEFIK_BACKEND} - traefik.enable: true - traefik.port: 8080 +app: + image: registry.webhosting.rug.nl/molgenis/molgenis:4.1.0 + ports: + - 8081:8080 + links: + - db + volumes_from: + - molgenis-data + labels: + io.rancher.sidekicks: molgenis-data + io.rancher.scheduler.global: true + traefik.frontend.rule: Host:${DOMAINS} + traefik.backend: ${TRAEFIK_BACKEND} + traefik.enable: true + traefik.port: 8080 - postgres: + db: 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: + expose: - 5432 + volumes_from: + - postgres-data 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: + 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 + - /opt/molgenis \ No newline at end of file diff --git a/templates/molgenis/3/rancher-compose.yml b/templates/molgenis/3/rancher-compose.yml index 373afc2..101efaf 100644 --- a/templates/molgenis/3/rancher-compose.yml +++ b/templates/molgenis/3/rancher-compose.yml @@ -1,6 +1,6 @@ .catalog: name: molgenis - version: v6.0.0 + version: v4.1.0 description: Molgenis minimum_rancher_version: v1.6.3 questions: @@ -25,4 +25,4 @@ unhealthy_threshold: 3 request_line: 'GET / HTTP/1.0' healthy_threshold: 2 - response_timeout: 5000 + response_timeout: 5000 \ No newline at end of file diff --git a/templates/molgenis/4/docker-compose.yml b/templates/molgenis/4/docker-compose.yml index ac963eb..43309fa 100644 --- a/templates/molgenis/4/docker-compose.yml +++ b/templates/molgenis/4/docker-compose.yml @@ -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 diff --git a/templates/molgenis/4/rancher-compose.yml b/templates/molgenis/4/rancher-compose.yml index f9e462f..a42daa3 100644 --- a/templates/molgenis/4/rancher-compose.yml +++ b/templates/molgenis/4/rancher-compose.yml @@ -1,6 +1,6 @@ .catalog: name: molgenis - version: v7.0.0 + version: v5.2.0 description: Molgenis minimum_rancher_version: v1.6.3 questions: @@ -25,4 +25,4 @@ unhealthy_threshold: 3 request_line: 'GET / HTTP/1.0' healthy_threshold: 2 - response_timeout: 5000 + response_timeout: 5000 \ No newline at end of file diff --git a/templates/molgenis/5/README.md b/templates/molgenis/5/README.md new file mode 100644 index 0000000..b65dd55 --- /dev/null +++ b/templates/molgenis/5/README.md @@ -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. \ No newline at end of file diff --git a/templates/molgenis/5/docker-compose.yml b/templates/molgenis/5/docker-compose.yml new file mode 100644 index 0000000..da54e3d --- /dev/null +++ b/templates/molgenis/5/docker-compose.yml @@ -0,0 +1,78 @@ + 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 diff --git a/templates/molgenis/5/rancher-compose.yml b/templates/molgenis/5/rancher-compose.yml new file mode 100644 index 0000000..373afc2 --- /dev/null +++ b/templates/molgenis/5/rancher-compose.yml @@ -0,0 +1,28 @@ +.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 diff --git a/templates/molgenis/6/README.md b/templates/molgenis/6/README.md new file mode 100644 index 0000000..b65dd55 --- /dev/null +++ b/templates/molgenis/6/README.md @@ -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. \ No newline at end of file diff --git a/templates/molgenis/6/docker-compose.yml b/templates/molgenis/6/docker-compose.yml new file mode 100644 index 0000000..ac963eb --- /dev/null +++ b/templates/molgenis/6/docker-compose.yml @@ -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 diff --git a/templates/molgenis/6/rancher-compose.yml b/templates/molgenis/6/rancher-compose.yml new file mode 100644 index 0000000..f9e462f --- /dev/null +++ b/templates/molgenis/6/rancher-compose.yml @@ -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 From cb70fb69826199e3f83c6ac275b72aa69a1919a6 Mon Sep 17 00:00:00 2001 From: sido Date: Thu, 15 Mar 2018 00:25:21 +0100 Subject: [PATCH 2/3] fix(docker-compose): replaced latest and stable at the right compose file --- templates/molgenis/0/docker-compose.yml | 4 ++-- templates/molgenis/1/docker-compose.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/molgenis/0/docker-compose.yml b/templates/molgenis/0/docker-compose.yml index 5f8871e..601cc58 100644 --- a/templates/molgenis/0/docker-compose.yml +++ b/templates/molgenis/0/docker-compose.yml @@ -1,5 +1,5 @@ molgenis: - image: registry.webhosting.rug.nl/molgenis/molgenis:stable + image: registry.webhosting.rug.nl/molgenis/molgenis:latest ports: - 8080 links: @@ -39,7 +39,7 @@ io.rancher.scheduler.global: true opencpu: - image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable + image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest ports: - 8004:8004 diff --git a/templates/molgenis/1/docker-compose.yml b/templates/molgenis/1/docker-compose.yml index 601cc58..5f8871e 100644 --- a/templates/molgenis/1/docker-compose.yml +++ b/templates/molgenis/1/docker-compose.yml @@ -1,5 +1,5 @@ molgenis: - image: registry.webhosting.rug.nl/molgenis/molgenis:latest + image: registry.webhosting.rug.nl/molgenis/molgenis:stable ports: - 8080 links: @@ -39,7 +39,7 @@ io.rancher.scheduler.global: true opencpu: - image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:latest + image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu:stable ports: - 8004:8004 From 5965a184a874559c6bd1091b7b9fbdb084d3758d Mon Sep 17 00:00:00 2001 From: sido Date: Thu, 15 Mar 2018 00:27:48 +0100 Subject: [PATCH 3/3] fix(docker-compose): added admin.password --- templates/molgenis/0/docker-compose.yml | 1 + templates/molgenis/1/docker-compose.yml | 1 + templates/molgenis/6/docker-compose.yml | 1 + 3 files changed, 3 insertions(+) diff --git a/templates/molgenis/0/docker-compose.yml b/templates/molgenis/0/docker-compose.yml index 601cc58..2e39cbe 100644 --- a/templates/molgenis/0/docker-compose.yml +++ b/templates/molgenis/0/docker-compose.yml @@ -12,6 +12,7 @@ - "db_driver=org.postgresql.Driver" - "db_user=molgenis" - "db_password=molgenis" + - "admin.password=admin" - "elasticsearch.cluster.name=molgenis" - "elasticsearch.transport.addresses=elasticsearch:9300" labels: diff --git a/templates/molgenis/1/docker-compose.yml b/templates/molgenis/1/docker-compose.yml index 5f8871e..3c82e4b 100644 --- a/templates/molgenis/1/docker-compose.yml +++ b/templates/molgenis/1/docker-compose.yml @@ -12,6 +12,7 @@ - "db_driver=org.postgresql.Driver" - "db_user=molgenis" - "db_password=molgenis" + - "admin.password=admin" - "elasticsearch.cluster.name=molgenis" - "elasticsearch.transport.addresses=elasticsearch:9300" labels: diff --git a/templates/molgenis/6/docker-compose.yml b/templates/molgenis/6/docker-compose.yml index ac963eb..7b1c877 100644 --- a/templates/molgenis/6/docker-compose.yml +++ b/templates/molgenis/6/docker-compose.yml @@ -12,6 +12,7 @@ - "db_driver=org.postgresql.Driver" - "db_user=molgenis" - "db_password=molgenis" + - "admin.password=admin" - "elasticsearch.cluster.name=molgenis" - "elasticsearch.transport.addresses=elasticsearch:9300" labels: