beacon4hcnv

Directory structure

beacon_test_data folder

• this directory contains CNV data to populate the database once it has been created. each file contains the data for the corresponding table

db folder

This folder contains the following files:

• db_schema.sql file that allow user to create an empty beacon4cnv database + functions.
• beacon4hcnv_db.backup to restore at once the structure of the database + the data for the CNV.

Database code

• Updating the counts of variants, samples and calls per dataset:

UPDATE beacon_dataset_table
SET variant_cnt=count_variants(id),
    call_cnt=count_calls(id),
    sample_cnt=count_samples(id);

Docker setup

Launch the following command on the beacon4hcnv folder

pip install docker-compose
docker build -t beacon4hcnv:latest .
docker-compose up -d db
docker-compose up -d beacon
docker-compose ps
docker-compose exec beacon sh
python -m beacon_api