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A Comprehensive Guide to Installing Pairtools
- Pairtools is a Python package for processing paired-end sequencing data, commonly used in bioinformatics for tasks such as Hi-C analysis.
- Installing Pairtools can be challenging due to dependency linking issues, particularly with pysam.
- The article provides a detailed guide on installing Pairtools successfully, avoiding common pitfalls like ImportError caused by broken library links.
- The installation guide is based on troubleshooting in a GitHub Codespace environment using Pairtools 1.1.3 and pysam 0.23.0.
- Pairtools is best suited for Unix-based systems, primarily Linux, but can be adapted for MacOS with similar steps.
- For Windows, a workaround method using tools like gcc is recommended for installation.
- The installation involves steps such as starting with a fresh Codespace, installing system dependencies, uninstalling existing packages, and building pysam from source.
- Verifications are done at various stages to ensure correct installation and linking of libraries.
- Testing Pairtools using the test suite is recommended to confirm a successful installation.
- The article also addresses troubleshooting common issues like linking errors, NumPy version warnings, and missing system dependencies.
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