bioinformatics-toolkits

Nix package registry for bioinformatics.

Usage

Run a tool directly without installing:

nix run github:SBEE-Lab/bioinformatics-toolkits#foldseek -- --help

Supported systems: x86_64-linux, aarch64-linux, aarch64-darwin.

As a flake input

Pull individual packages from packages.<system> — these are built against this repo's pinned nixpkgs, so results are reproducible:

{
  inputs.bio.url = "github:SBEE-Lab/bioinformatics-toolkits";

  outputs = { nixpkgs, bio, ... }: {
    # e.g. inside a devShell or package
    # bio.packages.x86_64-linux.foldseek
  };
}

Via the overlay

Use overlays.shared-nixpkgs to build the package set against your own nixpkgs instance:

{
  inputs.bio.url = "github:SBEE-Lab/bioinformatics-toolkits";

  outputs = { nixpkgs, bio, ... }:
    let
      pkgs = import nixpkgs {
        system = "x86_64-linux";
        overlays = [ bio.overlays.shared-nixpkgs ];
        config.allowUnfree = true; # required by nupack, psipred, …
      };
    in
    {
      # pkgs.bioinformatics-toolkits.foldseek, …
    };
}

Overlay packages build against your nixpkgs, not this repo's pin. That is usually fine, but if your nixpkgs is far from ours a dependency may not line up — pull from packages.<system> instead when you need the pinned build.

Available Packages

Structure

folddisco - Finding discontinuous motifs in protein structures

• License: GPL-3.0-or-later
• Homepage: https://github.com/steineggerlab/folddisco
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#folddisco -- --help
• Nix: packages/folddisco/package.nix

foldmason - Multiple protein structure alignment at scale with FoldMason

• License: GPL-3.0-or-later
• Homepage: https://github.com/steineggerlab/foldmason
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#foldmason -- --help
• Nix: packages/foldmason/package.nix

foldseek - Fast and sensitive protein structure search

• License: GPL-3.0-or-later
• Homepage: https://github.com/steineggerlab/foldseek
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#foldseek -- --help
• Nix: packages/foldseek/package.nix

structty - Interactive, terminal-native protein structure viewer

• License: GPL-3.0-only
• Homepage: https://github.com/steineggerlab/StrucTTY
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#structty -- --help
• Nix: packages/structty/package.nix

usalign - Universal structure alignment of monomeric and complex proteins and nucleic acids

• License: US-align license (permissive, BSD-like)
• Homepage: https://github.com/pylelab/USalign
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#usalign -- --help
• Nix: packages/usalign/package.nix

Sequence

dnachisel - Optimize DNA sequences under constraints

• License: MIT
• Homepage: https://github.com/Edinburgh-Genome-Foundry/DnaChisel
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#dnachisel -- --help
• Nix: packages/dnachisel/package.nix

mfeprimer - Check PCR primer specificity, dimers, hairpins, and other properties

• License: unfree
• Homepage: https://www.mfeprimer.com/
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#mfeprimer -- --help
• Nix: packages/mfeprimer/package.nix

nupack - Analysis and design of nucleic acid structures, devices, and systems

• License: unfree
• Homepage: https://www.nupack.org
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#nupack
• Nix: packages/nupack/package.nix

primer3 - PCR primer design and oligonucleotide analysis tools

• License: GPL-2.0-or-later / GPL-3.0-only
• Homepage: https://github.com/primer3-org/primer3
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#primer3 -- --help
• Nix: packages/primer3/package.nix

psipred - PSIPRED V4 protein secondary structure prediction

• License: unfree
• Homepage: https://github.com/psipred/psipred
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#psipred
• Nix: packages/psipred/package.nix

thermompnn - Predict ddG stability changes of protein point mutants with a ProteinMPNN-based GNN

• License: MIT
• Homepage: https://github.com/Kuhlman-Lab/ThermoMPNN
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#thermompnn -- --help
• Nix: packages/thermompnn/package.nix

Evolution

plmc - Infer Potts models (couplings) from a multiple sequence alignment by pseudo-likelihood maximization

• License: MIT
• Homepage: https://github.com/debbiemarkslab/plmc
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#plmc -- --help
• Nix: packages/plmc/package.nix

rate4site - Detect conserved amino-acid sites by computing the relative evolutionary rate for each site

• License: GPL-2.0-or-later
• Homepage: https://www.tau.ac.il/~itaymay/cp/rate4site.html
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#rate4site -- --help
• Nix: packages/rate4site/package.nix

Data

biomcp - Biomedical CLI and MCP server for biomedical data sources

• License: MIT
• Homepage: https://biomcp.org
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#biomcp -- --help
• Nix: packages/biomcp/package.nix

ncbi-datasets - NCBI command-line tool to gather data from NCBI databases

• License: publicDomain
• Homepage: https://github.com/ncbi/datasets
• Usage: nix run github:SBEE-Lab/bioinformatics-toolkits#ncbi-datasets -- --help
• Nix: packages/ncbi-datasets/package.nix

Library

biotite - Comprehensive library for computational molecular biology

• License: BSD-3-Clause
• Homepage: https://www.biotite-python.org
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#biotite
• Nix: packages/biotite/package.nix

dna-features-viewer - Plot features from DNA sequences

• License: MIT
• Homepage: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#dna-features-viewer
• Nix: packages/dna-features-viewer/package.nix

primer3-py - Python bindings for Primer3 primer design and oligonucleotide analysis

• License: GPL-2.0-or-later
• Homepage: https://github.com/libnano/primer3-py
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#primer3-py
• Nix: packages/primer3-py/package.nix

pydna - Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

• License: BSD-3-Clause
• Homepage: https://github.com/pydna-group/pydna
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#pydna
• Nix: packages/pydna/package.nix

snapgene-reader - Convert SnapGene files to dictionaries and Biopython records

• License: MIT
• Homepage: https://github.com/Edinburgh-Genome-Foundry/SnapGeneReader
• Usage: nix build github:SBEE-Lab/bioinformatics-toolkits#snapgene-reader
• Nix: packages/snapgene-reader/package.nix

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Run nix fmt before committing
4. Submit a pull request

License

Individual tools are licensed under their respective licenses.

The Nix packaging code in this repository is licensed under MIT.