Skip to content

INSTALLATION.md

Latest commit

 

History

History
104 lines (72 loc) · 1.78 KB

INSTALLATION.md

File metadata and controls

104 lines (72 loc) · 1.78 KB

Installation Guide

Quick Install

Using pip (recommended)

pip install umi-rna-simulator

From source

git clone https://github.com/lloydm/umi-rna-simulator.git
cd umi-rna-simulator
pip install -e .

Requirements

  • Python 3.10 or later
  • NumPy >= 1.20.0
  • SciPy >= 1.7.0

Development Installation

For development work, install with dev dependencies:

git clone https://github.com/lloydm/umi-rna-simulator.git
cd umi-rna-simulator
pip install -e .
pip install -r requirements-dev.txt

This includes:

  • pytest for running tests
  • pytest-cov for coverage reports
  • matplotlib for visualization (optional)

Verify Installation

# Check the CLI is available
umi-simulator --help

# Or use as Python module
python -m umi_simulator --help

# Run the test suite
pytest tests/

Optional: External Tools for Workflow Testing

For full workflow integration tests, you may want:

  • minimap2: RNA-seq alignment (recommended for M3 Mac compatibility)
  • UMI-tools: UMI extraction and deduplication
  • Subread/featureCounts: Gene quantification

Install on macOS

brew install minimap2
pip install umi-tools
brew install subread

Install on Linux

# Install minimap2
conda install -c bioconda minimap2

# Install UMI-tools
pip install umi-tools

# Install Subread
conda install -c bioconda subread

Troubleshooting

Import Error

If you get ModuleNotFoundError: No module named 'umi_simulator':

# Make sure you installed the package
pip install -e .

# Or add to PYTHONPATH temporarily
export PYTHONPATH="${PYTHONPATH}:/path/to/umi-rna-simulator"

Test Failures

If tests fail, ensure all dependencies are installed:

pip install -r requirements.txt
pip install -r requirements-dev.txt