Metadata-Version: 2.4
Name: oncotracer
Version: 2.1.0
Summary: Native, auditable LP-WGS CNA analysis for Illumina and Oxford Nanopore data
License-Expression: MIT
Author: OncoTracer developers
Requires-Python: >=3.10,<3.14
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Provides-Extra: paper
Provides-Extra: reports
Provides-Extra: variants
Requires-Dist: matplotlib (>=3.6) ; extra == "paper"
Requires-Dist: numpy (>=1.24) ; extra == "paper"
Requires-Dist: numpy (>=1.24) ; extra == "variants"
Requires-Dist: openpyxl (>=3.1) ; extra == "variants"
Requires-Dist: pysam (>=0.22) ; extra == "variants"
Requires-Dist: reportlab (>=4.0) ; extra == "reports"
Requires-Dist: reportlab (>=4.0) ; extra == "variants"
Requires-Dist: safetensors (>=0.4) ; extra == "reports"
Requires-Dist: scipy (>=1.10) ; extra == "variants"
Requires-Dist: torch (>=2.2) ; extra == "reports"
Requires-Dist: transformers (>=4.51,<5) ; extra == "reports"
Project-URL: Documentation, https://cfarkas.github.io/oncotracer/
Project-URL: Homepage, https://github.com/cfarkas/oncotracer
Project-URL: Issues, https://github.com/cfarkas/oncotracer/issues
Project-URL: Source, https://github.com/cfarkas/oncotracer
Description-Content-Type: text/markdown

# OncoTracer

OncoTracer analyzes Illumina and Oxford Nanopore reads for DNA copy-number changes and optional small variants. Configure samples, choose Fresh or FFPE preservation, and review results through its browser interface. For research use.

## Install

OncoTracer supports 64-bit Linux and Python 3.10–3.13. Install the command in your Python environment:

```bash
pip install oncotracer
```

No Git checkout is required. Pip installs the application and its bundled workflow resources. Choose one backend to prepare and verify the scientific tools before analysis.

With Conda available:

```bash
oncotracer install --conda
oncotracer --interactive --backend conda
```

With Docker running and accessible:

```bash
oncotracer install --docker
oncotracer --interactive --backend docker
```

Choose the sequencing platform and **Fresh** or **FFPE** inside the browser, then select inputs, settings and a project folder. Save and check before choosing Run. Optional callers, models and licensed annotation resources are configured separately.

For concurrent analyses, open another terminal and use a different project/output folder. Sessions select available browser ports; allocate CPU and memory for each run.

## Uninstall

To remove an additional global launcher while keeping scientific tools and projects:

```bash
oncotracer uninstall --global-launcher --yes
python -m pip uninstall oncotracer
```

Use the Python environment where you installed the package for the pip command. To remove managed scientific tools too, first preview `oncotracer uninstall --conda --dry-run` and then use `oncotracer uninstall --conda --yes`.

## Documentation

- [Installation and backend requirements](https://cfarkas.github.io/oncotracer/installation/)
- [Browser setup](https://cfarkas.github.io/oncotracer/setup/)
- [Variants and FFPE resources](https://cfarkas.github.io/oncotracer/variants/)
- [Nextflow entry point](https://cfarkas.github.io/oncotracer/nextflow_entry/)
- [Source and issues](https://github.com/cfarkas/oncotracer)

