From 40b912ff00927a19fbdf04adec3e5778dd2ead0d Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Sat, 10 Mar 2018 12:25:59 +0100
Subject: [PATCH] feat(added new versions): added version 6 and 7 to the
 molgenis catalogue

---
 templates/molgenis/2/docker-compose.yml  |  7 ++-
 templates/molgenis/3/docker-compose.yml  |  7 ++-
 templates/molgenis/4/README.md           | 16 +++++
 templates/molgenis/4/docker-compose.yml  | 78 ++++++++++++++++++++++++
 templates/molgenis/4/rancher-compose.yml | 28 +++++++++
 5 files changed, 134 insertions(+), 2 deletions(-)
 create mode 100644 templates/molgenis/4/README.md
 create mode 100644 templates/molgenis/4/docker-compose.yml
 create mode 100644 templates/molgenis/4/rancher-compose.yml

diff --git a/templates/molgenis/2/docker-compose.yml b/templates/molgenis/2/docker-compose.yml
index 6def96a..6d15632 100644
--- a/templates/molgenis/2/docker-compose.yml
+++ b/templates/molgenis/2/docker-compose.yml
@@ -1,5 +1,5 @@
   molgenis:
-    image: webhost12.service.rug.nl/molgenis/molgenis:5.2.0
+    image: registry.webhosting.rug.nl/molgenis/molgenis:5.2.0
     ports:
       - 8080
     links:
@@ -50,6 +50,11 @@
 #    labels:
       #io.rancher.sidekicks: elasticsearch-data
 
+  opencpu:
+    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu
+    ports:
+      - 8004:8004
+
   postgres-data:
     image: busybox
     labels:
diff --git a/templates/molgenis/3/docker-compose.yml b/templates/molgenis/3/docker-compose.yml
index 2bf5bf1..3484860 100644
--- a/templates/molgenis/3/docker-compose.yml
+++ b/templates/molgenis/3/docker-compose.yml
@@ -1,5 +1,5 @@
   molgenis:
-    image: webhost12.service.rug.nl/molgenis/molgenis:6.0.0
+    image: registry.webhosting.rug.nl/molgenis/molgenis:6.0.0
     ports:
       - 8080
     links:
@@ -51,6 +51,11 @@
       #io.rancher.sidekicks: elasticsearch-data
       io.rancher.scheduler.global: true
 
+  opencpu:
+    image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu
+    ports:
+      - 8004:8004
+
   postgres-data:
     image: busybox
     labels:
diff --git a/templates/molgenis/4/README.md b/templates/molgenis/4/README.md
new file mode 100644
index 0000000..b65dd55
--- /dev/null
+++ b/templates/molgenis/4/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/4/docker-compose.yml b/templates/molgenis/4/docker-compose.yml
new file mode 100644
index 0000000..4ea59ab
--- /dev/null
+++ b/templates/molgenis/4/docker-compose.yml
@@ -0,0 +1,78 @@
+  molgenis:
+    image: registry.webhosting.rug.nl/molgenis/molgenis:7.0.0
+    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
+
+    opencpu:
+      image: registry.webhosting.rug.nl/molgenis/molgenis-opencpu
+      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/4/rancher-compose.yml b/templates/molgenis/4/rancher-compose.yml
new file mode 100644
index 0000000..373afc2
--- /dev/null
+++ b/templates/molgenis/4/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