GDI Starter Kit - Luxembourgish deployment

Getting started

This repository was created to help you get started with GDI Starter Kit (https://github.com/GenomicDataInfrastructure), based on experiences of Luxembourgish node.

We would like to provide you with:

• some notes that we took when deploying components of the GDI Starter Kit
• an all-in-one Docker compose script to get you started fast
• some instructions on what to do next (regarding configuration or loading the data)

Generally, each repository for Starter Kit components contains already a readme file with exact steps to be taken to successfully deploy. In this repository, we cloned all the original source code and modified them to have only one compose script. You can review the individual readme and compose files to check the relevant notes and how-to instructions.

Status

This project is ongoing and not fully operational yet. The instructions should get you a running Beacon, REMS, htsget, and a nginx reverse proxy. Running Storages and interfaces and loading the data might require some more hacking.

Components

Component	Original repository	Short description
REMS	link	Resource Entitlement Management System to manage access rights to datasets
Beacon	link	A discoverability service - an API to query for variants, individuals etc.
LS:AAI mock	link	Mock of Life Sciences AAI. Not needed if you created LS:AAI OIDC client.
Storages and Interfaces	link	Set of components related to storage of datasets (e.g. minio)
htsget	link	Server to stream sensitive genomics data

While a reverse proxy is not a part of original Starter Kit, we added it for the convenience (nginx).

Instructions

Preparatory

# Create a docker network
docker network create my-app-network

# Create and prepare REMS database
docker compose -f docker-compose-rems.yml up -d rems_db
docker compose -f docker-compose-rems.yml run --rm -e CMD="migrate" rems_app

Starting the services for the first time

(Assuming that the REMS database is up)

docker compose -f docker-compose-rems.yml up -d rems_app
docker compose -f docker-compose-beacon.yml up -d
docker compose -f docker-compose-htsget.yml up -d
docker compose -f docker-compose-storage-and-interfaces.yml up -d
docker compose -f docker-compose-nginx.yml up -d

Note: Storages and interfaces project will require additional steps which are not yet fully documented here. Please find some our notes in the README_STORAGE_AND_INTERFACES.md. Moreover, getting the synthetic data in will also require some additional work.

Starting the services another time

(Assuming that the REMS database is down)

docker compose -f docker-compose-rems.yml up -d
docker compose -f docker-compose-beacon.yml up -d
docker compose -f docker-compose-htsget.yml up -d
docker compose -f docker-compose-storage-and-interfaces.yml up -d
docker compose -f docker-compose-nginx.yml up -d

Alternatively, you can use:

docker compose -f docker-compose.yml up -d

Stopping the services

docker compose -f docker-compose-rems.yml down
docker compose -f docker-compose-beacon.yml down
docker compose -f docker-compose-htsget.yml down
docker compose -f docker-compose-storage-and-interfaces.yml down
docker compose -f docker-compose-nginx.yml down

docker compose -f docker-compose.yml down

Modifications and notes

If you are interested in what modifications were made compared to the original repositories, take a look in the relevant readme files, e.g.:

• REMS
• Beacon