Docker images for MOLGENIS applications.
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.
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
git clone https://github.com/molgenis/docker.git
Ctrl-C in the terminal
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
.env file or export the variables in shell.
Example for .env file:
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
Comment out the "app" section of the
If the data seems to be loaded, press
ctrl+c to gracefully shut down the containers.
Revert the changes you did in your
Restart your docker using:
*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
*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:
Determine the id of your postgres container:
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