Installation

Overview

MicroHapulator depends on several Python packages and bioinformatics tools. Using conda to install and manage these packages and their dependencies is recommended. See this page for instructions on configuring conda to enable installing packages from the bioconda channel.

conda create --name microhapulator -y python=3.8 microhapulator
conda activate microhapulator
mhpl8r --help

To test whether installation was successful, pytest is recommended.

conda install -y pytest
pytest --pyargs microhapulator

Dependencies

MicroHapulator depends on several Python packages. These are listed in setup.py in the main source code distribution. If performing a non-standard installation with pip, these dependencies will automatically be installed from the Python Package Index (PyPI).

Preparing Illumina reads for analysis and interpretation with MicroHapulator also depends on several bioinformatics tools, including FLASH, BWA (or an alternative short read aligner), SAMtools, and FastQC. These software tools are installed automatically when performing a standard installation with Conda. Otherwise, they must be installed manually.

Development quick start

If you're setting up an environment for developing MicroHapulator, you may want to skip the procedure outlined above and use the following instead.

conda create --new microhapulator python=3.8 flash bwa samtools fastqc
conda activate microhapulator
git clone https://github.com/bioforensics/MicroHapulator.git
cd MicroHapulator/
pip install -e .  # Install the package and its Python dependencies
make devdeps      # Install development packages
make devhooks     # Register pre-commit hooks for development