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
- 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
- To install datasources-etl and set up the entry points fun:
pip install .
- To execute a rule using snakemake:
snakemake ${RULE_NAME}