Ligase
Type-safe, reproducible computational biology pipelines. A Rust core with a Python surface.
Biological data types carry dimensions — organism, reference build,
coordinate system, sample set — and the engine refuses to connect steps whose
dimensions do not match, the way a physics engine refuses to add metres to
seconds. The worst comp bio bugs are silent: hg19 vs hg38 mix-ups, 0- vs
1-based coordinates, chr1 vs 1, shuffled sample IDs. Workflow tools move
files; Ligase understands them.
Status: v0.1.0. All six v0.1 milestones are done — the type system, the graph, the content-addressed cache, semantic hashing and audit mode, provenance, and validation against published resistance results. See docs/milestones.md for what each one had to prove.
Intended use
Ligase is research software. The drug-resistance calls in its reference pipeline come from applying the Stanford HIVdb algorithm to variants Ligase called, and they are not for clinical use — not for diagnosis, not for treatment decisions, and not a substitute for a validated clinical assay or a clinician's judgement.
The validation in M6 checks Ligase's calls against published results on two public datasets. That is evidence the implementation is faithful to the algorithm. It is not evidence that it is fit for patient care, and it was never meant to be.
Install
pip install ligase-bio
Wheels cover Linux, macOS and Windows for Python 3.11 and newer, so this needs no compiler. Building from source instead needs a Rust toolchain and a C compiler, because SQLite is compiled from bundled source — see the installation guide.
For development:
git clone git@github.com:Neoforge-Labs/ligase.git && cd ligase
pip install -e ".[dev]"
Names
| Thing | Name |
|---|---|
| Rust core crate | ligase |
| PyPI distribution | ligase-bio |
| Python import | ligase |
Licence
Dual-licensed under either MIT or Apache-2.0, at your option.
1 maintainer
Metadata
1 maintainer
Release files for ligase-bio 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| ligase_bio-0.1.0.tar.gz | 314.8 kB | With provenance | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| ligase_bio-0.1.0-cp311-abi3-win_amd64.whl | CPython 3.11 | abi3 | Windows x86-64 | Details |
| ligase_bio-0.1.0-cp311-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.11 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| ligase_bio-0.1.0-cp311-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.11 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| ligase_bio-0.1.0-cp311-abi3-macosx_11_0_arm64.whl | CPython 3.11 | abi3 | macOS 11.0+ ARM64 | Details |
| ligase_bio-0.1.0-cp311-abi3-macosx_10_12_x86_64.whl | CPython 3.11 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 11.3 MB
Release files / ligase_bio-0.1.0.tar.gz
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| Tags | Source |
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