datasources-etl

This repository contains scripts developed as part of an exploration of data required for initial mapping and the scripts required to automate data acquisition and transformation tasks to populate a Crash Move Folder.

A few assumptions for development:

• Scripts are developed in Python
• Data transformations rely, where possible, exclusively on Python libraries or shell one-liners

Setting up the environment

• Create a conda environment and activate it:

conda create --name datasources-etl 
activate datasources-etl 

• Install the requirements:

conda install -c conda-forge -c bioconda --file requirements.txt

• Some packages are not available through conda. Install them using pip:

pip install -r requirements-pip.txt 

Installing and Running

• To install datasources-etl and set up the entry points fun:

pip install .

• To execute a rule using snakemake:

snakemake ${RULE_NAME}