christianhilbrands / docker

Dockerfiles and docker-compose for MOLGENIS

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. Else elastic search will give indexing errors. 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/<latest_version>

You can see what the latest version is in the molgenis folder, for example 10.0.

Start MOLGENIS

docker-compose up

Navigate to http://localhost:80/ in your browser (http://localhost:8081/ for versions before MOLGENIS 8.2).

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

Start MOLGENIS with profiles

From MOLGENIS 8.7 and up you can use profiles to turn on optional functionality. The available profiles are described in the README in each version's folder.

docker-compose --profile audit --profile opencpu up

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 

Start a docker with an existent database dump

Add volumes to your database in docker (db section of docker-compose file):

  - /directory/to/dbdump/on/your/machine:/docker-entrypoint-initdb.d

Comment out the "app" section of the docker-compose file.

docker-compose up

If the data seems to be loaded, press ctrl+c to gracefully shut down the containers.

Revert the changes you did in your docker-compose file.

Restart your docker using:

docker-compose up

*Note: this is just for restoring a database dump, the filestore is not included.

Making db dump from docker

If you want to make a database dump from your docker to use somewhere else, add this line in the volumes of the db section of the docker-compose file:

  - /directory/to/save/your/dump/in/on/your/machine:/dump

*Note: it's best if the directory you choose to configure here is empty as it will be linked to your docker container

Now you can start your molgenis docker the way you are used to:

docker-compose up

Determine the id of your postgres container:

docker ps

Copy the id of the postgres container.

docker exec -it yourCopiedId bash

Now you can create your database dump.

pg_dump -U molgenis > /dump/yourpgdump.sql

The data will be stored in the directory you configured in the docker-compose file.