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Installation

pathotypr ships as a native desktop app, a command-line binary, and as source you can build yourself.

Desktop GUI (pre-built)

Download the latest release

Then pick the file for your platform:

Platform File Notes
macOS (Apple Silicon) Pathotypr_<version>_aarch64.dmg M1 / M2 / M3 / M4 Macs
macOS (Intel) Pathotypr_<version>_x64.dmg Pre-2020 Macs
Linux (.deb) Pathotypr_<version>_amd64.deb Debian / Ubuntu
Linux (.rpm) Pathotypr-<version>-1.x86_64.rpm Fedora / RHEL
Linux (AppImage) Pathotypr_<version>_amd64.AppImage Any distro, no install needed
Windows (installer) Pathotypr_<version>_x64-setup.exe Windows 10+
Windows (.msi) Pathotypr_<version>_x64_en-US.msi Windows 10+ (MSI)

Older versions are on the releases page.

First launch on macOS and Windows

The app is not signed with a paid developer certificate, so the OS may warn you the first time you open it.

  • macOS: right-click the app → Open → click Open in the dialog. See Apple support for details.
  • Windows: if SmartScreen appears, click More info → Run anyway.

CLI (Bioconda)

conda create -n pathotypr -c bioconda pathotypr
conda activate pathotypr
pathotypr --help

From source

git clone https://github.com/PathoGenOmics-Lab/pathotypr.git
cd pathotypr
cargo build --release -p pathotypr-core --bin pathotypr
./target/release/pathotypr --help

Requirements

A recent Rust toolchain (stable). No other system dependencies are needed for the CLI.

Most people should download the app instead

Ready-built installers are published for every release — see Desktop GUI (pre-built) above. Build from source only if you are modifying pathotypr itself.

# Development build with hot reload
cargo tauri dev

# Production build (installers/bundles)
cargo tauri build

The GUI has additional system dependencies (WebView, etc.). See the Desktop GUI guide for the full per-platform setup.

MTBC marker files & pre-trained model

Ready-to-use marker panels and a pre-trained Random Forest model for Mycobacterium tuberculosis complex (MTBC) are published on Zenodo:

File Description
pathotypr_lineage_markers_*.tsv 3,707 lineage SNPs (L1–L10, A1–A4)
pathotypr_dr_markers_ancestor_*.tsv DR mutations from the WHO catalogue (2nd edition, 2023), in ancestor coordinates
pathotypr_dr_markers_H37Rv_*.tsv The same catalogue in H37Rv coordinates
pathotypr_rf_model_*.pathotypr Pre-trained RF model (k=31, 100 trees)

DOI

10.5281/zenodo.19210043

Once installed, head to the command guides or the input formats reference to get started.