Hackathon Setup¶

Clone ClawBio, set up your Python environment, and verify everything works by running a demo skill.

1. Clone the Repository¶

git clone https://github.com/ClawBio/ClawBio.git
cd ClawBio

2. Create a Virtual Environment¶

python3 -m venv .venv
source .venv/bin/activate  # Linux/macOS
# .venv\Scripts\activate   # Windows

3. Install Dependencies¶

pip3 install -r requirements.txt

Core dependencies: pandas, numpy, matplotlib, seaborn.

Optional (for specific skills):

pip3 install scanpy          # scRNA-seq skills
pip3 install reportlab       # PDF report generation
pip3 install pydeseq2        # RNA-seq differential expression
pip3 install bioblend        # Galaxy Bridge

4. Run a Demo¶

Verify everything works by running a built-in demo:

# Pharmacogenomics demo
python3 skills/pharmgx-reporter/pharmgx_reporter.py \
  --input skills/pharmgx-reporter/demo_patient.txt \
  --output /tmp/pharmgx_demo

# Check the output
cat /tmp/pharmgx_demo/report.md

You should see a pharmacogenomics report with drug recommendations. If this works, your environment is ready.

Troubleshooting¶

`ModuleNotFoundError: No module named 'pandas'`¶

You forgot to activate the virtual environment or install dependencies. Run pip install -r requirements.txt.

`Permission denied` on output directory¶

Create the output directory first: mkdir -p /tmp/my_output.

macOS: `xcrun: error: invalid active developer path`¶

Install Xcode command line tools: xcode-select --install.

Ready? Move on to Your First Skill.