47 lines
1.5 KiB
Nix
47 lines
1.5 KiB
Nix
{lib, stdenv, fetchurl, fetchFromGitHub, cmake, boost179, gmp, htslib, zlib, xz, pkg-config}:
|
|
|
|
stdenv.mkDerivation rec {
|
|
pname = "octopus";
|
|
version = "0.7.4";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "luntergroup";
|
|
repo = "octopus";
|
|
rev = "v${version}";
|
|
sha256 = "sha256-FAogksVxUlzMlC0BqRu22Vchj6VX+8yNlHRLyb3g1sE=";
|
|
};
|
|
|
|
nativeBuildInputs = [ cmake pkg-config ];
|
|
buildInputs = [ boost179 gmp htslib zlib xz ];
|
|
|
|
patches = [ (fetchurl {
|
|
url = "https://github.com/luntergroup/octopus/commit/17a597d192bcd5192689bf38c5836a98b824867a.patch";
|
|
sha256 = "sha256-VaUr63v7mzhh4VBghH7a7qrqOYwl6vucmmKzTi9yAjY=";
|
|
}) ];
|
|
|
|
postPatch = ''
|
|
# Disable -Werror to avoid build failure on fresh toolchains like
|
|
# gcc-13.
|
|
substituteInPlace lib/date/CMakeLists.txt --replace-fail ' -Werror ' ' '
|
|
substituteInPlace lib/ranger/CMakeLists.txt --replace-fail ' -Werror ' ' '
|
|
substituteInPlace lib/tandem/CMakeLists.txt --replace-fail ' -Werror ' ' '
|
|
substituteInPlace src/CMakeLists.txt --replace-fail ' -Werror ' ' '
|
|
|
|
# Fix gcc-13 build due to missing <cstdint> header.
|
|
sed -e '1i #include <cstdint>' -i src/core/tools/vargen/utils/assembler.hpp
|
|
'';
|
|
|
|
postInstall = ''
|
|
mkdir $out/bin
|
|
mv $out/octopus $out/bin
|
|
'';
|
|
|
|
meta = with lib; {
|
|
description = "Bayesian haplotype-based mutation calling";
|
|
mainProgram = "octopus";
|
|
license = licenses.mit;
|
|
homepage = "https://github.com/luntergroup/octopus";
|
|
maintainers = with maintainers; [ jbedo ];
|
|
platforms = platforms.x86_64;
|
|
};
|
|
}
|