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{ lib, stdenv, fetchFromGitHub, zlib }:
stdenv.mkDerivation {
pname = "bwa";
version = "unstable-2022-09-23";
src = fetchFromGitHub {
owner = "lh3";
repo = "bwa";
rev = "139f68fc4c3747813783a488aef2adc86626b01b";
hash = "sha256-8u35lTK6gBKeapYoIkG9MuJ/pyy/HFA2OiPn+Ml2C6c=";
};
buildInputs = [ zlib ];
# Avoid hardcoding gcc to allow environments with a different
# C compiler to build
preConfigure = ''
sed -i '/^CC/d' Makefile
'';
makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
# it's unclear which headers are intended to be part of the public interface
# so we may find ourselves having to add more here over time
installPhase = ''
runHook preInstall
install -vD -t $out/bin bwa
install -vD -t $out/lib libbwa.a
install -vD -t $out/include bntseq.h
install -vD -t $out/include bwa.h
install -vD -t $out/include bwamem.h
install -vD -t $out/include bwt.h
runHook postInstall
'';
meta = with lib; {
description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";
mainProgram = "bwa";
license = licenses.gpl3Plus;
homepage = "https://bio-bwa.sourceforge.net/";
maintainers = with maintainers; [ luispedro ];
platforms = platforms.unix;
};
}
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