blob: 801ad00876bf5dd05c4e68cbf747713351d870ad (
plain) (
blame)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
|
{ lib, stdenv, fetchurl, fetchpatch, zlib }:
stdenv.mkDerivation rec {
pname = "bwa";
version = "0.7.17";
src = fetchurl {
url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";
sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
};
patches = [
# Pull upstream patch for -fno-common toolchain support like upstream
# gcc-10: https://github.com/lh3/bwa/pull/267
(fetchpatch {
name = "fno-common.patch";
url = "https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch";
sha256 = "1lihfxai6vcshv5vr3m7yhk833bdivkja3gld6ilwrc4z28f6wqy";
})
];
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 = ''
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;
};
}
|