EJP-RD - NBIS demo setup

Note: This repository contains serveral git submodules that lock in specific versions of data and configurations located in other repositories. When you have used git clone or git checkout _____ please remember to update the submodules.

git submodule init
git submodule update

Running using docker-compose

Common preparation

Create persistent docker networks that can be used to connect services:

docker network create ejprd-oidc
docker network create ejprd-public
docker network create ejprd-secure

GDI Starter Kit services:

Run the following commands or see documentation for htsget and storage and interfaces configuration and usage:

docker compose --project-directory config/gdi-starter-kit up -d

EJP-RD Services

Run the following command or see documentation for FAIR Data Point and EJP-RD Beacon configuration and usage:

docker compose --project-directory config/fair-in-a-box up -d

Utilities

Run the following command or see documentation for Jupyter Lab configuration and usage:

docker compose --project-directory config/notebook up -d

Status

This repo will contain

• Test data, created by the EJP-RD NBIS team
  • [ ] Variant data (VCF/BCF)
• Instructions on how to set up and test the different GDI components
  • [x] htsget
  • [ ] lsaai-mock
  • [ ] rems
  • [x] storage-and-interfaces
  • [ ] beacon-v2
  • [ ] containerized-computations
• and the (EJP-RD) components
  • [x] FDP (metadata, DCAT-AP)
  • [x] EJP-RD Beacon for CARE-SM data
  • [ ] SPARQL endpoint/ rdf store (data in CARE-SM model)
• Instructions on how to import the data to sda, beacon, and the rdf store.
• An example containerized-computation work flow, where
  • [ ] beacon and the sparql endpoints are used to find interesting data
  • [ ] htsget is used to retrieve the data
  • [ ] some computation is performed
  • [ ] the output is a link to the result

htsget, beacon and the sparql endpoint should be accessible from within the containerised compute environment to stage the data necessary for the analysis.

If needed, parts of this can be mocked.