Rfam Production Code

About

This repository provides a set of tools related to the Rfam production pipeline. The collection includes script for data export, database processing, visualisation and validation, as well as detailed Rfam release documentation.

Scripts

• Export: Data export tools
• Processing: Database processing tools
• View: Rfam family view process related scripts
• Validation: Data validation scripts
• Utils: Support modules/utilities

Using with Docker

• build container

  docker build -t rfam-production .

• open bash interactive shell

  docker run -v `pwd`:/rfam/rfam-production -it rfam-production bash

• run a command inside the container

  docker run -v `pwd`:/rfam/rfam-production -it rfam-production python scripts/export/rfam_xml_dumper.py --out /rfam --type C

Installation

# install Python dependencies
pip install -r requirements.txt

# set up Python path
export PYTHONPATH=/path/to/the/project

# create and edit configuration file (excluded from version control)
cp config/rfam_local_template.py config/rfam_local.py

Contact us

Feel free to submit an issue if you have any questions or suggestions.