Installation

Installation

Requirements

• Linux or macOS
• Mash 2.0 or later (installed automatically with conda)
• Python 3.10 or later with numpy, pandas, scipy, scikit-bio (≥ 0.7), plotly and openpyxl

With pip

pip install genome-comparator
genome-comparator --version

Mash is not available from PyPI and must be installed separately, for example with conda install -c bioconda mash, or from the Mash releases. genome-comparator finds mash in your PATH, or next to the Python interpreter it runs with.

From source with conda

git clone https://github.com/duceppemo/genome_comparator
cd genome_comparator
conda env create -f environment.yml
conda activate genome_comparator
pip install --no-deps .
genome-comparator --version

environment.yml only uses the conda-forge and bioconda channels. It requires gsl>=2.8 because older bioconda builds of Mash fail to start with newer GSL versions (see Troubleshooting).

Development install

Use an editable install so changes to the code are used right away, then run the tests:

pip install --no-deps -e .
pytest

The end-to-end tests are skipped if mash is not in your PATH.

Without installing

The commands can also be run directly from the cloned folder, as long as the dependencies are available (the main command with python3 -m genome_comparator):

python3 -m genome_comparator -h
python3 dendrogram_from_distance_matrix.py -h
python3 tree_collapser.py -h
python3 tree_renamer.py -h

Updating from 0.4.3 or earlier

The main command was renamed from mash-phylo to genome-comparator in version 0.4.4, with the same options. mash-phylo still works but prints a deprecation warning; update your scripts.

Updating from 0.2 or earlier

Version 0.3.0 requires Python ≥ 3.10 and scikit-bio ≥ 0.7. Recreate your environment:

conda env remove -n genome_comparator
conda env create -f environment.yml