Merge pull request #22 from imperial-genomics-facility/doc_update

Doc update

README.md

@@ -1 +1,83 @@
-# IGFPortal
+# 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, integrating data pipelines, and visualizing results, particularly in genomics research.
+
+## Key Features
+- **Project Management**: Track sequencing projects, sequencing runs, samplesheets and analysis metadata, improving organization and facilitate validation.
+- **Pipeline Integration**: Automates genomic data processing, enabling seamless integration with bioinformatics workflows. Provides easy to use interface for triggering data pipelines.
+- **Result Visualization**: Offers an intuitive interface with graphical views for data analysis results and project status. Utilises Redis caching to minimise loading analysis reports.
+
+## Requirements
+- **Docker**: For containerized deployments
+
+## Installation
+
+**1. Clone the Repository**
+
+```bash
+git clone https://github.com/imperial-genomics-facility/IGFPortal.git
+
+cd IGFPortal
+```
+
+**2. Create an environment file**
+
+Create a new file `env` and add the following lines:
+
+```
+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 config file**
+
+Copy the `nginx_template.conf` to `nginx.conf` and replace `server_name` value.
+
+```
+server {
+    # Redirect http to https
+    listen 80 default_server;
+    server_name SERVER_ADDRESS;
+    return 301 https://$server_name$request_uri;
+}
+```
+
+**4. Build docker image**
+
+```bash
+docker build -t imperialgenomicsfacility/igfportal:v0.0.2.1 .
+```
+
+**5. Update docker compose file**
+
+Update `docker-compose.yaml` file and add correct path for following:
+
+  * Path of the local copy of IGFPortal repo (default is /home/vmuser/github/IGFPortal)
+  * Path for SSL certs (default is /home/vmuser/github/ssl)
+  * Path for static directory (default is ./static)
+  * Path for Apache Airflow connection conf (default /home/vmuser/secrets/airflow_conf.json)
+
+**6. Start the server using docker compose**
+
+```bash
+  PORTAL_UID="$(id -u)" GID="$(id -g)"  docker compose -f docker-compose.yaml -p igfportal up -d
+```
+
+**7. Access the Portal**
+
+Open your browser at `https://SERVER_ADDRESS` to access the IGFPortal dashboard.
+
+## License
+
+This project is licensed under the Apache-2.0 License. See the [LICENSE](LICENSE) file for details.