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Biopkgs

Biopkgs is a collection of packages for the Nix package manager. This collection contains mainly bioinformatic applications and libraries, and it is maintained independently from the official Nixpkgs tree because

  1. Biopkgs will keep multiple versions of each package to facilitate reproducibility of research results.
  2. Biopkgs will add or update packages in a rolling manner.
  3. Biopkgs will not require that packages be split into modular pieces, nor will it require that packages be always compiled against shared libraries.

Nix is a suitable package manager for fast-paced research software development, because it natively allows for multiple versions of packages (especially C and C++ libraries). Its requirement for full specification of package dependencies within a functional framework facilitates code compilation across Unix-like platforms.

Requirement

Installation

There is propbably a smarter way of distributing this package collection, but for now, you should clone the repository in your $HOME directory:

cd
git clone https://github.com/djhshih/biopkgs

Then, you may list the available packages in Biopkgs by

nix-env -f ~/biopkgs -qa

To install a package (e.g. samtools), run

nix-env -f ~/biopkgs -i samtools

Docker images

Nix scripts to build docker images are found in pkgs/docker-images. These images may be built using bin/dockerize.sh.

See also

Nix Package Manager Guide
Nixpkgs Contributors Guide

Contribute

Submit a pull request for each package. Please ensure that your package builds successfully before submitting.