428045f39b
Without the change build fails on -fno-common toolchains like upstream
gcc-10 as:
$ nix build -L --impure --expr 'with import ./. {}; bwa.overrideAttrs (oa: { NIX_CFLAGS_COMPILE = (oa.NIX_CFLAGS_COMPILE or "") + "-fno-common"; })'
...
ld: ./libbwa.a(rope.o):/build/bwa-0.7.17/rle.h:33:
multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
ld: ./libbwa.a(rle.o):/build/bwa-0.7.17/rle.h:33:
multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
50 lines
1.6 KiB
Nix
50 lines
1.6 KiB
Nix
{ lib, stdenv, fetchurl, fetchpatch, zlib }:
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stdenv.mkDerivation rec {
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pname = "bwa";
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version = "0.7.17";
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src = fetchurl {
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url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";
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sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
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};
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patches = [
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# Pull upstream patch for -fno-common toolchain support like upstream
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# gcc-10: https://github.com/lh3/bwa/pull/267
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(fetchpatch {
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name = "fno-common.patch";
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url = "https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch";
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sha256 = "1lihfxai6vcshv5vr3m7yhk833bdivkja3gld6ilwrc4z28f6wqy";
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})
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];
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buildInputs = [ zlib ];
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# Avoid hardcoding gcc to allow environments with a different
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# C compiler to build
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preConfigure = ''
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sed -i '/^CC/d' Makefile
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'';
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makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
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# it's unclear which headers are intended to be part of the public interface
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# so we may find ourselves having to add more here over time
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installPhase = ''
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install -vD -t $out/bin bwa
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install -vD -t $out/lib libbwa.a
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install -vD -t $out/include bntseq.h
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install -vD -t $out/include bwa.h
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install -vD -t $out/include bwamem.h
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install -vD -t $out/include bwt.h
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'';
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meta = with lib; {
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description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";
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license = licenses.gpl3;
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homepage = "http://bio-bwa.sourceforge.net/";
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maintainers = with maintainers; [ luispedro ];
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platforms = platforms.x86_64;
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};
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}
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