Docker image for LOVD server

Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for Gene-centered collection and display of DNA variations. LOVD version 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.

This Docker image provides stable LOVD installation with Apache 2 web server, PHP. Database management system (such as MySQL) should be in another Docker container. The docker-compose tool helps deploying all required container (see docker-compose.yml file).

Installing docker-compose

sudo pip install --upgrade pip
sudo pip install docker-compose

Runing image

Edit docker-compose.yml before. It will work with no modification for testing purpose.

For db container:

• MYSQL_DATABASE name of database for LOVD
• MYSQL_USER user for LOVD
• MYSQL_PASSWORD password for LOVD MySQL user

For lovd container:

• LOVD_DB_NAME user for LOVD (same of MYSQL_USER)
• LOVD_DB_PASSWORD password for LOVD MySql user (same of MYSQL_PASSWORD)
• LOVD_DB_NAME name of database for LOVD (same of MYSQL_DATABASE)
• LOVD_TABLE_PREFIX prefix of LOVD tables (default is lovd)
• LOVD_BASEDIR accept access to LOVD via custom base URL for multiple sites

The MYSQL_USER and MYSQL_PASSWORD are defined in .env file. This file should be owned by root user wihout access by others.

docker-compose up -d

Stop containers

docker-compose down

Database will still avaibable at db_data volume. To stop containers and delete volumes run.

docker-compose down --volumes

Building image

git clone git@github.com:labbcb/docker-lovd.git
cd docker-lovd
docker image build --tag welliton/lovd .