9bb3fccb5b
continuation of #109595 pkgconfig was aliased in 2018, however, it remained in all-packages.nix due to its wide usage. This cleans up the remaining references to pkgs.pkgsconfig and moves the entry to aliases.nix. python3Packages.pkgconfig remained unchanged because it's the canonical name of the upstream package on pypi.
45 lines
1.3 KiB
Nix
45 lines
1.3 KiB
Nix
{ lib, stdenv, cmake, rocksdb, rapidjson, pkg-config, fetchFromGitHub, fetchpatch, zlib }:
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stdenv.mkDerivation rec {
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pname = "sortmerna";
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version = "4.2.0";
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src = fetchFromGitHub {
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repo = pname;
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owner = "biocore";
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rev = "v${version}";
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sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
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};
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nativeBuildInputs = [ cmake pkg-config ];
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buildInputs = [ zlib rocksdb rapidjson ];
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cmakeFlags = [
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"-DCMAKE_BUILD_TYPE=Release"
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"-DPORTABLE=off"
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"-DRAPIDJSON_HOME=${rapidjson}"
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"-DROCKSDB_HOME=${rocksdb}"
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"-DROCKSDB_STATIC=off"
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"-DZLIB_STATIC=off"
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];
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postPatch = ''
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# Fix formatting string error:
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# https://github.com/biocore/sortmerna/issues/255
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substituteInPlace src/sortmerna/indexdb.cpp \
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--replace 'is_verbose, ss' 'is_verbose, "%s", ss'
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# Fix missing pthread dependency for the main binary.
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substituteInPlace src/sortmerna/CMakeLists.txt \
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--replace "target_link_libraries(sortmerna" \
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"target_link_libraries(sortmerna Threads::Threads"
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'';
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meta = with lib; {
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description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
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license = licenses.lgpl3;
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platforms = platforms.x86_64;
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homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
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maintainers = with maintainers; [ luispedro ];
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};
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}
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