Install Framework using Singularity/Apptainer

For quick installation on environments where Docker is not available (such as HPC clusters), you can use Singularity/Apptainer. This guide assumes Singularity/Apptainer is already installed on your system.

Setup Process

1. Database Setup

The Makefile in ./scripts/apptainer/Makefile provides easy environment setup:

cd ./scripts/apptainer
make full-setup

This command will: - Download and run a PostgreSQL container through Singularity/Apptainer - Load database dumps by executing the load_dumps.sh script

2. Container Management

Once the database is ready: - Stop the container: make down - Start it again: make up

3. Dependencies Installation

Install all required dependencies using conda:

conda env create -f ./scripts/apptainer/environment.yml
conda activate pids

Running the Framework

Once both the database and conda environment are ready, run the framework with:

python pidsmaker/main.py SYSTEM DATASET --artifact_dir ./artifacts/ --database_host localhost