HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
HTSeq you will need:
Python >= 3.4(tested up to 3.6)
pysam >= 0.9.0
To run the
htseq-qa script, you will also need:
To build the package from source, you will also need:
The latter packages are not required if you have already built
and are transferring the binaries onto another machine with a compatible
environment (architechture, shared libraries). If you are not sure,
chances are you need them.
Both Linux and OSX are supported and binaries are provided for virtually
all Linux versions and for some OSX versions (the latter only for Python 2.7
and 3.6). A source package which should not require
is provided for all other cases.
Windows is not officially supported as we don't have access to a Continuous
Integration Windows machine that supports
pysam. However, if you have built
HTSeq for Windows, please open an issue and we'll try and include it in the
To install directly from PyPI:
pip install HTSeq
To install a specific version (e.g. version 0.11.0):
pip install 'HTSeq==0.11.0'
If this fails, please install all dependencies first:
pip install 'matplotlib>=1.4' pip install Cython pip install 'pysam>=0.9' pip install HTSeq
pysam==0.9.0 has a bug so that
pip Cython is
required at installation.
pysam>=0.10.0 should build without
Using setup.py (distutils/setuptools)
Install the dependencies with your favourite tool (
HTSeq itself, run:
python setup.py build install