Prerequisites

In order to run the docker version of EVAdb in a secure and performant manner, some prerequisites need to be fulfilled. Please make sure that you have a basic understanding of docker and how the web works before setting up this website.

In order to follow setup and usage guides, it is important that you have an understanding on docker, SSL certificates (for https) and the performance of the system you are hosting your database at.

Physical Infrastructure

Hardware Requirements

To be able to host EVAdb, the hardware must have:

• 4TB NVMe/SSD Storage

Additional performance improvements are gained by utilizing more RAM and CPU Power.

EVAdb is meant to host multiple thousand exome cases. As is the case with such datasets, even storing only variants will have the database growing to be multiple terabytes in size. In order to have a nice user experience for the frontend, it is important that the backend database does not bog down even for large requests (f.e. all autosomal dominant variants for one sample). To be able to scale the amount of data, we recommend a physical server utilizing NVMe (or at least SSD) storage technologies. This will greatly increase the database performance for all queries. Make sure you have enough storage available for the expected amount of data. The initialized application will consume around 400GB without any cases added.

Spinning Rust

We advise heavily against running the databse on older HDD type storage media. Performance will be abysmal.

Docker

Docker

Docker is a isolation technique prevalent in modern software development since it allows the automatic deployment of complex software stacks.

Read more: Docker Get Started

Docker Setup

To be able to host EVAdb through Docker Images, make sure you have installed and correctly configured:

1. Docker
2. docker-compose

If you desire to install the application via Docker, please familiarize yourself with the basic concepts of Docker. To deploy the application, we use docker-compose which allows us to deploy the stack of multiple containers through use of a single command.

Please follow the installation instructions for docker on your favorite operating system over at docker.com. Some operating systems might need additional setup after installation of docker, typically adding the active user to the docker group. Make sure you follow these steps as well (postinstallation). To be able to continue with the installation guide, please also install docker-compose.

SSL Certificates

SSL Certificates

Obtaining a certificate and private key pair is necessary to host EVAdb. Make sure you have obtained a pair and named them evadb.crt and evadb.key to run the application.

SSL is used in https to encrypt connections to remote servers. In order to validate the servers identity to the client, the server needs to present a valid certificate. Valid certificates can be obtained from letsencrypt or your local universities IT department. To run EVAdb, you have to supply a certificate for use by the web service.

Letsencrypt

In order to use the following letsencrypt description, your server needs to be reachable from the Internet and have a known DNS entry.

In order to request a valid certificate from letsencrypt, you can use the certbot application. It can be installed on any UNIX-like machine through the package manager of choice. Once installed, use

certbot certonly --standalone

to get a certificate for your server.

For development purposes, it is enough to create a self-signed certificate. On UNIX-like machines the openssl tool can be used to create a self-signed certificate for use with EVAdb.

openssl req -x509 -newkey rsa:4096 \
    -keyout evadb.key \
    -out  evadb.crt\
    -days 365 \
    --nodes

This will print your certificate and its private key at evadb.key and evadb.crt respectively. These should be placed in the secrets folder, that will be passed into the docker-containers for the user and admin frontends.