Python-based web application for metaproteomic analysis of microbiome samples

• Python 3.4+
• Flask
• Pandas/NumPy
• PostgreSQL 9.4+ (local or remote)
• see requirements.txt for details

• Clone this repo and cd into root (biome) directory
• Create a virtualenv: $ pyvenv venv
• Activate virtualenv: $ source venv/bin/activate
• Install dependencies: (venv) $ pip install -r requirements.txt
• Create PostgreSQL database. Access Postgres with psql and run: CREATE DATABASE biome;
• Create database tables: (venv) $ python manage.py db upgrade
• Config can be set using the $BIOME_CONFIG environment variable (see config.py)
• Run (dev) server: (venv) $ python manage.py runserver

(optional, but needed for some functionality)

• Launch Redis: redis-server (connection details are in config.py)
• Launch Celery worker (can launch in the foreground using a second terminal window)
  • Activate venv in new terminal: $ source venv/bin/activate
  • Launch worker process: (venv) $ celery worker -A biome.celery --loglevel=info

• Create PostgreSQL testing database. Access Postgres with psql and run: CREATE DATABASE biometesting;
• Change to root (biome) directory and run: (venv) $ python -m unittest discover