Installation

To install the python package, use a clean Python 3 environment and run:

pip install --upgrade pip
pip install "git+https://github.com/debbiemarkslab/BEAR.git"

Preprocessing fasta and fastq files requires installation of KMC. This code has been tested on KMC version 3.1.1. Mac and Linux users should run ulimit -n 2048 to allow KMC to make a large number of files; otherwise the preprocessing stage may fail with a File not found error. The folder with the KMC binaries should be added to the path; for instance, run export PATH="LOCATION/KMC3.1.1:$PATH" on Mac/Linux.

To test your installation, run pytest in the project directory. All tests should pass.