molgenis-solve-rd's Introduction

Molgenis Solve RD Database

The purpose of the RD3 database is to track and find samples processed by Centro Nacional De Análisis Genómico (CNAG) and submited to the European Genome-phenome Archive (EGA). For more information, follow the links below.

The Solve-RD project site: http://solve-rd.eu
RD3 Data Model repository: https://github.com/molgenis/RD3_database

What's in this repository?

The molgenis-solve-rd repository contains all of the scripts and other files for maintaining the RD3 database.

data/: This folder contains various EMX files for entities that were added after the initial release
public/: This folder contains the custom molgenis apps that are used in the Molgenis database. Additional information can be found in the public/README.md file.
python/: Various python scripts for prcessing data and other jobs
R/: Various R scripts for processing data and other jobs
shell/: scripts for importing data into Molgenis
www/: various static assets (i.e., images, documents, etc.)

In addition, the archive folder has files that I'm not ready to remove. The dev folder is exlained in the following section.

Getting Started

Configuring R

In the dev folder, you will find the dev.R file. Use this file to configure the R workspace.

If you are working with R scripts, you will need to initialize the R library on your local machine. This workspace uses renv to manage R packages. Run the following command in the R console to initialize the R library locally.