Installation

Requirements

gaftools has the following requirement:

• python>=3.9

• pysam

• pywfa

The users do not need to explicitly install the requirements. The requirements are installed as part of the pip installation step.

The documentation is built using sphinx (only installed installed automatically in development mode installation of gaftools).

Building from Source

Unreleased development versions of gaftools can be installed by building from source:

pip install git+https://github.com/marschall-lab/gaftools

We recommend installing inside a conda environment to allow easy removal:

conda create -n gaftools-env python=3.10
conda activate gaftools-env
pip install git+https://github.com/marschall-lab/gaftools

If you already have a clone locally, then run:

git clone https://github.com/marschall-lab/gaftools
conda create -n gaftools-env python=3.10
conda activate gaftools-env
cd gaftools
pip install .

To remove gaftools, the conda environment needs to be removed using:

conda env remove -n gaftools-env

gaftools can be used with python>=3.8

Installing from PyPI

gaftools is now available on PyPI and can be installed with:

pip install gaftools

We recommend installation inside a clean conda environment to allow easy removal and avoid dependency issues. For example, to install gaftools in a conda environment named gaftools-env, run the following commands:

conda create -n gaftools-env python=3.10
conda activate gaftools-env
pip install gaftools

Installing from Conda

gaftools is now available on bioconda and can be installed with:

conda install bioconda::gaftools

We recommend installation inside a clean conda environment to allow easy removal and avoid dependency issues. For example, to install gaftools in a conda environment named gaftools-env, run the following commands:

conda create -n gaftools-env python=3.10
conda activate gaftools-env
conda install bioconda::gaftools