hap-py: cleanup, fix cmake 4 compatibility (#468825) (a6fbd6cb) · Commits · nix / nixpkgs

pkgs/by-name/ha/hap-py/package.nix

+27 −13

Original line number	Diff line number	Diff line
		@@ -37,22 +37,26 @@ let
		];
		my-python = python3.withPackages my-python-packages;
		in
		stdenv.mkDerivation rec {
		stdenv.mkDerivation (finalAttrs: {
		pname = "hap.py";
		version = "0.3.15";

		src = fetchFromGitHub {
		owner = "Illumina";
		repo = "hap.py";
		rev = "v${version}";
		tag = "v${finalAttrs.version}";
		hash = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";
		};
		# For illumina script
		BOOST_ROOT = "${boost.out}";
		ZLIBSTATIC = "${zlib.static}";
		# For cmake : boost lib and includedir are in different location
		BOOST_LIBRARYDIR = "${boost.out}/lib";
		BOOST_INCLUDEDIR = "${boost.dev}/include";

		# CMake 4 dropped support of versions lower than 3.5,
		# versions lower than 3.10 are deprecated.
		# https://github.com/NixOS/nixpkgs/issues/445447
		postPatch = ''
		substituteInPlace CMakeLists.txt \
		--replace-fail \
		"cmake_minimum_required (VERSION 2.8)" \
		"cmake_minimum_required (VERSION 3.10)"
		'';

		patches = [
		# Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
		@@ -76,17 +80,27 @@ stdenv.mkDerivation rec {
		zlib
		];

		env = {
		# For illumina script
		BOOST_ROOT = "${boost.out}";
		ZLIBSTATIC = "${zlib.static}";

		# For cmake : boost lib and includedir are in different location
		BOOST_LIBRARYDIR = "${boost.out}/lib";
		BOOST_INCLUDEDIR = "${boost.dev}/include";
		};

		postFixup = ''
		wrapProgram $out/bin/hap.py \
		--set PATH ${lib.makeBinPath runtime} \
		--add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"
		--add-flags "--engine-vcfeval-path=${lib.getExe rtg-tools}"
		'';

		meta = with lib; {
		meta = {
		description = "Compare genetics variants against a gold dataset";
		homepage = "https://github.com/Illumina/hap.py";
		license = licenses.bsd2;
		maintainers = with maintainers; [ apraga ];
		license = lib.licenses.bsd2;
		maintainers = with lib.maintainers; [ apraga ];
		mainProgram = "hap.py";
		};
		}
		})

pkgs/by-name/rt/rtg-tools/package.nix

+7 −6

Original line number	Diff line number	Diff line
		@@ -11,14 +11,14 @@
		unzip,
		}:

		stdenv.mkDerivation rec {
		stdenv.mkDerivation (finalAttrs: {
		pname = "rtg-tools";
		version = "3.13";

		src = fetchFromGitHub {
		owner = "RealTimeGenomics";
		repo = "rtg-tools";
		rev = version;
		rev = finalAttrs.version;
		hash = "sha256-vPzKrgnX6BCQmn9aOVWWpFLC6SbPBHZhZ+oL1LCbvmo=";
		};

		@@ -59,11 +59,12 @@ stdenv.mkDerivation rec {
		ant runalltests
		'';

		meta = with lib; {
		meta = {
		homepage = "https://github.com/RealTimeGenomics/rtg-tools";
		description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";
		license = licenses.bsd2;
		license = lib.licenses.bsd2;
		platforms = [ "x86_64-linux" ];
		maintainers = with maintainers; [ apraga ];
		maintainers = with lib.maintainers; [ apraga ];
		mainProgram = "rtg";
		};
		}
		})

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