HTSeq Installation

HTSeq is a Python library for analyzing high-throughput sequencing data.

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  1. Install via PIP

  • To install the latest version from PyPI:

pip install HTSeq

  • To install a specific version (e.g., 2.0.0):

pip install 'HTSeq==2.0.0'

  • If this fails, make sure all dependencies are installed first:

pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq

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  1. Install via setup.py (distutils/setuptools)

  1. Install dependencies with your preferred tool (pip, conda, etc.).

  2. Install HTSeq:

python setup.py build install

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  1. Testing

  • To test the full HTSeq installation locally:

./test.sh

  • To test htseq-count alone:

htseq-count -o output_file input_file

  • A virtual environment is created in the .venv folder, and HTSeq is installed inside it, including all modules and scripts.