IGFPortal

IGFPortal is a web-based data management and analysis tool created by the NIHR Imperial BRC Genomics Facility. It facilitates tracking and managing genomic sequencing projects, integrates with data pipelines, and provides tools for visualizing results.

Key features

• Project management: track sequencing projects, runs, samplesheets, and analysis metadata.
• Pipeline integration: automates genomic data processing and integrates with bioinformatics workflows.
• Result visualization: offers an intuitive interface with graphical views for results and project status. Uses Redis caching to reduce load times.

Requirements

• Docker (for containerized deployments)
• Optional: Docker Compose

Installation

1. Clone the repository:

git clone https://github.com/imperial-genomics-facility/IGFPortal.git
cd IGFPortal

2. Create an environment file

Create a new file named env and add:

PYTHONPATH=/container_path/IGFPortal
FLASK_APP=/container_path/IGFPortal/app/__init__.py
SQLALCHEMY_DATABASE_URI=mysql+pymysql://DBUSER:DBPASS@DB/MYSQL_DATABASE
MYSQL_ROOT_PASSWORD=MYSQL_ROOT_PASSWORD
MYSQL_DATABASE=MYSQL_DATABASE
MYSQL_USER=DBUSER
MYSQL_PASSWORD=DBPASS
BASIC_AUTH=FlowerUser:FlowerUserPass
CELERY_BROKER_URL=redis://redis_db/0
CELERY_RESULT_BACKEND=redis://redis_db/1
CACHE_REDIS_URL=redis://redis_db/2
CELERY_WORK_DIR=/TMP_WORK_DIR_FOR_CELERY_WORKER
AIRFLOW_CONF_FILE=/container_path/secret/airflow_conf.json

3. Create nginx configuration

Copy nginx_template.conf to nginx.conf and update the server_name:

cp nginx_template.conf nginx.conf
# Edit nginx.conf and replace SERVER_ADDRESS

Example (for HTTP -> HTTPS redirect):

server {
    listen 80 default_server;
    server_name SERVER_ADDRESS;
    return 301 https://$server_name$request_uri;
}

4. Build the Docker image:

docker build -t imperialgenomicsfacility/igfportal:v3.0.0 .

5. Update docker-compose.yaml

Update paths in docker-compose.yaml to match your environment:

• Path for SSL certs (default: ../ssl_cert)
• Path for static directory (../static)
• Path for Airflow connection conf (default: ../secret/airflow_conf.json)

6. Start the server using Docker Compose:

PORTAL_UID="$(id -u)" GID="$(id -g)" \
docker compose \
-f docker-compose-prod.yaml \
-p igfportal up -d

7. Access the portal

Open your browser at https://SERVER_ADDRESS.

License

This project is licensed under the Apache-2.0 License. See the LICENSE file for details.