Workflow for JUMP dataset

This repository contains the source code to reproduce the preprocessing workflow for COMPOUND, CRISPR and ORF data from the JUMP dataset.

Installation

We suggest uv for environment management. The following commands create the environment from scratch and install the required packages.

uv sync
uv pip install -e .
source .venv/bin/activate

Get data

Download profiles and metadata for compound (crispr or orf):

source download_data.sh compound

Run workflow

snakemake -c1 --configfile inputs/config/compound.json

Testing

To run the tests, first set your PYTHONPATH to include the repository root:

export PYTHONPATH=$(pwd)
pytest

The test suite includes an integration test to verify the pipeline's functionality using a minimal dataset.