Installation

Using pip

You can install haptools from PyPI using pip.

pip install haptools

Installing haptools with the “files” extra requirements enables automatic support for a variety of additional file formats, like PLINK2 PGEN files.

pip install 'haptools[files]'

Note

Installing haptools with the “files” extra requirement requires gcc and a few other compiler tools. Please make sure that they are installed first. To install with conda, for example, please execute the following:

conda install -c conda-forge gxx_linux-64

Alternatively, you can use the following on Ubuntu:

sudo apt install build-essential

See issue 217 for current progress on this problem.

Using conda

We also support installing haptools from bioconda using conda.

conda install -c conda-forge -c bioconda haptools

Note

Installing haptools from bioconda with PGEN support is not yet possible. See issue 228 for current progress on this challenge.

Installing the latest, unreleased version

Can’t wait for us to tag and release our most recent updates? You can install haptools directly from the main branch of our Github repository using pip.

pip install --upgrade --force-reinstall git+https://github.com/cast-genomics/haptools.git