Installation

Installation With Mamba

Install Mambaforge, Miniforge, or another conda-compatible distribution with mamba, then create the environment:

git clone https://github.com/rotheconrad/chromosort.git
cd chromosort

mamba env create -f environment.yml
mamba activate chromosort

The environment installs:

• Python
• minimap2
• MUMmer 4 (nucmer, delta-filter, show-coords)
• Pillow for optional PNG plot output
• pytest for the test suite
• ChromoSort command-line tools

Installation With Pixi

If you prefer Pixi, ChromoSort also ships a pixi.toml environment file:

git clone https://github.com/rotheconrad/chromosort.git
cd chromosort

pixi install
pixi run help
pixi run test

The Pixi environment uses the same conda-forge/bioconda stack as environment.yml, including Python, minimap2, MUMmer 4, Pillow, pytest, and the ChromoSort command-line tools.

Why Pillow Is Included

chromo plot writes PDF and SVG plots directly. PNG output is different because it is a raster image format, so ChromoSort uses Pillow when --formats png is requested. This keeps PNG export inside Python and avoids requiring separate system renderers such as Cairo, ImageMagick, browser engines, or SVG-to-PNG conversion tools. Pillow is not used by the sorting, fixing, scaffolding, or gap-filling algorithms.

Verify the Install

chromo --help
chromo sort --help
chromo clean --help
chromo fix --help
chromo cut --help
chromo manual --help
chromo plot --help
chromo scaffold --help
chromo gapfill --help

For development checks, run:

pytest
# or
pixi run test