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Getting started

Give DART a quick try!

For a quick test drive of DART you can access a demo account with limited features on our public instance (in case you get logged out the username/password is demo). You can try out the following:

  • Run a query in real-time using a predefined panel/query on the samples of our demo dataset published on zenodo
  • Explore the variants resulting from the query
  • Look at a sample report and download it in csv and json format
  • Load a report JSON in the viewer (available also without login)

Install and use a local stand-alone instance

Requirements and pre-requisites

This workflow was tried on MacOS Mojave and on a Linux Debian distribution.

You must have DOCKER installed and running on your machine: for LINUX please be sure that both the docker and docker-compose packages are installed. We suggest to dedicate at least 2 CPUs and 4GB of RAM to the Docker daemon. The complete installation files, data input files and database files need around 30GB of space on disk.

Installation

Download and extract the lastet release binary DART-server-1.0.0-install.tar.gz:

wget --no-http-keep-alive https://github.com/DanieleBarreca/BSF_DART/releases/download/1.0.0/DART-server-1.0.0-install.tar.gz
tar -xzvf DART-server-1.0.0-install.tar.gz

Start the application server

To start the application server you can use the start script:

bash DART-server-1.0.0/start.sh

Please note that the server log is under DATA/log/server.log. The server can take some time before being up and running.

DO NOT remove the installation folder DART-server-1.0.0 since all the data resides here!

In the DATA folder of the installation folder you will find:

  • A log folder where the application server logs are written
  • A mongo folder where the mongodb files are written
  • A mysql folder where the mysql files are written
  • A projects folder where your project data reside

Download and load the demo data

To load data on your local installation of DART you should create a project in your installation folder under DATA/projects and then run the loader (make sure the application server is up and running).

To download and extract our demo trio project (https://doi.org/10.5281/zenodo.4314874), you can use the following:

cd DART-server-1.0.0
wget --no-http-keep-alive https://zenodo.org/record/4320863/files/DART_Demo_Trio.tar.gz
tar -xzf DART_Demo_Trio.tar.gz

Once the project is extracted in the DATA/projects folder you can load it in DART using the command from terminal

docker exec -it dart-server './bin/dart_loader/loader.sh' 'DART_Demo_Trio'

Access the tool

Open your browser (tested with Google Chrome and Firefox) on localhost:8080 and login using the credentials:

  • User: DART_user
  • Password: changeme

You can refer to the guides in this documentation for usage details.

Stopping the application server

To stop the application server you can use the stop script:

bash DART-server-1.0.0/stop.sh

Uninstallation

  1. Remove all the docker images (container are removed by the stop script) docker image rm org.open.medgen/dart-server:1.0.0_local
  2. Remove all the data stored locally rm -r DART-server-1.0.0

Source code avaialbility

For more details regarding software architecture and configuration, as well as the complete source code of DART, please refer to our GITHUB repository.