Installation

genomepy requires Python 3.7+

You can install genomepy via bioconda, pip or git.

Bioconda

$ conda install -c conda-forge -c bioconda 'genomepy>=0.15'

Pip

$ pip install genomepy

With the Pip installation, you will have to install additional dependencies, and make them available in your PATH.

To read/write bgzipped genomes you will have to install pysam.

If you want to use gene annotation features, you will have to install the following utilities:

genePredToBed
genePredToGtf
bedToGenePred
gtfToGenePred
gff3ToGenePred

You can find the binaries here.

Git

$ git clone https://github.com/vanheeringen-lab/genomepy.git
$ conda env create -n genomepy -f genomepy/environment.yml
$ conda activate genomepy
$ pip install -e genomepy