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nixpkgs/pkgs/applications/science/biology/bwa/default.nix
Profpatsch 4a7f99d55d treewide: with stdenv.lib; in meta -> with lib;
Part of: https://github.com/NixOS/nixpkgs/issues/108938

meta = with stdenv.lib;

is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.

This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.

The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
2021-01-11 10:38:22 +01:00

39 lines
1.1 KiB
Nix

{ lib, stdenv, fetchurl, zlib }:
stdenv.mkDerivation rec {
pname = "bwa";
version = "0.7.17";
src = fetchurl {
url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";
sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
};
buildInputs = [ zlib ];
# Avoid hardcoding gcc to allow environments with a different
# C compiler to build
preConfigure = ''
sed -i '/^CC/d' Makefile
'';
# 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 = ''
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
'';
meta = with lib; {
description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";
license = licenses.gpl3;
homepage = "http://bio-bwa.sourceforge.net/";
maintainers = with maintainers; [ luispedro ];
platforms = platforms.x86_64;
};
}