Merge pull request #326174 from t4ccer/t4/sratoolkit-3.1.1 (bc95156d) · Commits · mdf / nixpkgs

pkgs/applications/science/biology/sratoolkit/default.nix

deleted100644 → 0

+0 −56

Original line number	Diff line number	Diff line
		{ stdenv
		, lib
		, fetchurl
		, autoPatchelfHook
		, libidn
		, zlib
		, bzip2
		}:


		let
		libidn11 = libidn.overrideAttrs (old: {
		pname = "libidn";
		version = "1.34";
		src = fetchurl {
		url = "mirror://gnu/libidn/libidn-1.34.tar.gz";
		sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p";
		};
		});

		in

		stdenv.mkDerivation rec {
		pname = "sratoolkit";
		version = "2.11.3";

		src = fetchurl {
		url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${version}/sratoolkit.${version}-ubuntu64.tar.gz";
		sha256 = "1590lc4cplxr3lhjqci8fjncy67imn2h14qd2l87chmhjh243qvx";
		};

		nativeBuildInputs = [
		autoPatchelfHook
		];

		buildInputs = [
		libidn11
		zlib
		bzip2
		stdenv.cc.cc.lib
		];

		sourceRoot = "sratoolkit.${version}-ubuntu64/bin";

		installPhase = ''
		find -L . -executable -type f -! -name "remote-fuser" -exec install -m755 -D {} $out/bin/{} \;
		'';

		meta = with lib; {
		homepage = "https://github.com/ncbi/sra-tools";
		description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives";
		license = licenses.ncbiPd;
		maintainers = with maintainers; [ thyol ];
		platforms = [ "x86_64-linux" ];
		};
		}

0 → 100644

+40 −0

Original line number	Diff line number	Diff line
		{
		lib,
		stdenv,
		fetchFromGitHub,
		bison,
		cmake,
		doxygen,
		flex,
		graphviz,
		python3,
		}:

		stdenv.mkDerivation (finalAttrs: {
		pname = "ncbi-vdb";
		version = "3.1.1";

		src = fetchFromGitHub {
		owner = "ncbi";
		repo = "ncbi-vdb";
		rev = "refs/tags/${finalAttrs.version}";
		hash = "sha256-HBiheN8XfYYwmY5gw7j8qTczn6WZZNTzY2/fGtpgs/8=";
		};

		nativeBuildInputs = [
		bison
		cmake
		doxygen
		flex
		graphviz
		python3
		];

		meta = {
		homepage = "https://github.com/ncbi/ncbi-vdb";
		description = "Libraries for the INSDC Sequence Read Archives";
		license = lib.licenses.ncbiPd;
		maintainers = with lib.maintainers; [ t4ccer ];
		platforms = lib.platforms.unix;
		};
		})

0 → 100644

+57 −0

Original line number	Diff line number	Diff line
		{
		stdenv,
		lib,
		fetchFromGitHub,
		cmake,
		python3,
		bison,
		flex,
		libxml2,
		openjdk,
		ncbi-vdb,
		mbedtls,
		}:

		stdenv.mkDerivation (finalAttrs: {
		pname = "sratoolkit";

		# NOTE: When updating make sure to update ncbi-vdb as well for versions to match
		version = "3.1.1";

		src = fetchFromGitHub {
		owner = "ncbi";
		repo = "sra-tools";
		rev = "refs/tags/${finalAttrs.version}";
		hash = "sha256-WVPiAz3EFYuhBnl7BsEjJ2BTi1wAownEunVM4sdLaj8=";
		};

		cmakeFlags = [
		"-DVDB_INCDIR=${ncbi-vdb}/include"
		"-DVDB_LIBDIR=${ncbi-vdb}/lib"
		];

		buildInputs = [
		ncbi-vdb
		libxml2
		mbedtls
		];

		nativeBuildInputs = [
		cmake
		python3
		bison
		flex
		openjdk
		];

		meta = {
		homepage = "https://github.com/ncbi/sra-tools";
		description = "Collection of tools and libraries for using data in the INSDC Sequence Read Archives";
		license = lib.licenses.ncbiPd;
		maintainers = with lib.maintainers; [
		thyol
		t4ccer
		];
		platforms = lib.platforms.unix;
		};
		})

+0 −2

Original line number	Diff line number	Diff line
		@@ -17453,8 +17453,6 @@ with pkgs;

		srandrd = callPackage ../tools/X11/srandrd { };

		sratoolkit = callPackage ../applications/science/biology/sratoolkit { };

		srecord = callPackage ../development/tools/misc/srecord { };

		srelay = callPackage ../tools/networking/srelay { };