Docker

Docker images for MOLGENIS applications.

Requirements

• Git

• Docker

• Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

• Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1