wassermanlab/GUD

Genomic Unification Database

Genomic Unification Database

This is a database which centralizes and unifies genomic data in a universal manner for specific reference datasets.

Manifest

• GUD/ORM - Object relational mapping classes
• GUD/parsers - Parsers for upserting data into GUD
• GUD/scripts - General scripts

Requirements

GUD requires the following dependencies:

• GNU Core Utilities
• MySQL
• Python ≥2.7 or 3.x (recommended) with:
  • Biopython
  • Core API
  • flask
  • Flask-SQLAlchemy
  • FuzzyWuzzy
  • interval-binning
  • NumPy
  • pandas
  • pybedtools
  • PyMySQL
  • pyliftover
  • requests
  • SQLAlchemy
  • SQLAlchemy-FullText-Search
  • SQLAlchemy-Utils

Configuration

conda create -n gud -c bioconda -c conda-forge python=3.7 biopython coreutils flask \
    flask-sqlalchemy fuzzywuzzy pandas pymysql pyliftover python-coreapi requests
pip install flask-limiter interval-binning python-Levenshtein SQLAlchemy-FullText-Search \
    sqlalchemy-utils

START UP SERVER

export FLASK_APP=GUD/api
export FLASK_ENV=development
flask run