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 for your platform:
| Platform | Download | Notes |
|---|---|---|
| macOS (Apple Silicon) | Pathotypr_1.0.0_aarch64.dmg | M1 / M2 / M3 / M4 Macs |
| macOS (Intel) | Pathotypr_1.0.0_x64.dmg | Pre-2020 Macs |
| Linux (.deb) | Pathotypr_1.0.0_amd64.deb | Debian / Ubuntu |
| Linux (.rpm) | Pathotypr-1.0.0-1.x86_64.rpm | Fedora / RHEL |
| Linux (AppImage) | Pathotypr_1.0.0_amd64.AppImage | Any distro, no install needed |
| Windows (installer) | Pathotypr_1.0.0_x64-setup.exe | Windows 10+ |
| Windows (.msi) | Pathotypr_1.0.0_x64_en-US.msi | Windows 10+ (MSI) |
All builds 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)¶
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.
# 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 | Download |
|---|---|---|
pathotypr_lineage_markers_v1.0.0.tsv |
3,707 lineage SNPs (L1–L10, A1–A4) | Download |
pathotypr_dr_markers_v1.0.0.tsv |
102,213 DR mutations (WHO catalogue 2021) | Download |
pathotypr_rf_model_v1.0.0.pathotypr |
Pre-trained RF model (k=31, 100 trees) | Download |
Once installed, head to the command guides or the input formats reference to get started.