Installation¶

gmeta is a Python 3.12 package driving external bioinformatics tools. Two installation paths cover every scenario:

pixi (recommended)pip

The repo ships a pixi.toml that pins every external tool — kraken2, bracken, sylph, fastp, minimap2, bowtie2, samtools — plus the Python package itself:

git clone https://github.com/indexofire/gmeta
cd gmeta
pixi install          # default env: tools + gmeta
pixi run -e dev test  # dev env: + pytest/ruff/pyright/mkdocs

The parser/report layer is pure Python; only gmeta run and coverage computation shell out to external binaries:

pip install gmeta     # needs click/pydantic/jinja2/openpyxl/weasyprint

Tools are resolved from PATH (or GMETA_PIXI_BIN); PDF output additionally requires a system pango.

What lands where¶

Path	Contents
`src/gmeta/data/`	Chinese name tables, priority pathogen list
`src/gmeta/templates/`	Jinja2 report template (HTML and PDF share it)
`$GMETA_DB_DIR`	databases (repo: `<repo>/data/db`; installed: `~/.local/share/gmeta/db`)

Next steps¶

Quick start — first sample end to end
Databases — kraken2/bracken/sylph/reference setup