Installation

Install Format Policy

ChromoSort intentionally supports more than one install style. Use mamba or conda when you want the familiar scientific Python plus bioconda stack. Use Pixi when you prefer Pixi’s project task runner and lockable environment workflow. Use a plain Python editable install for lightweight code work in generic automation harnesses.

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
pixi run agent-check

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.

When pixi.toml changes, the matching pixi.lock should be refreshed and committed so Pixi users get a reproducible environment.

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 eval all --help
chromo fix --help
chromo cut --help
chromo manual --help
chromo gafprep --help
chromo plot --help
chromo scaffold --help
chromo gapfill --help

For development checks, run:

make agent-check
# or, from a Pixi environment
pixi run agent-check
# or the underlying test suite
python -m unittest discover -s tests -v
# pytest is also fine when available
pytest
# legacy Pixi test task
pixi run test