62 lines
1.6 KiB
Nix
62 lines
1.6 KiB
Nix
{ lib
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, stdenv
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, cmake
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, rocksdb_8_3
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, rapidjson
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, pkg-config
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, fetchFromGitHub
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, zlib
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}:
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let
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rocksdb = rocksdb_8_3;
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in
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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${version}";
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sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
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};
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nativeBuildInputs = [ cmake pkg-config ];
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buildInputs = [ zlib rocksdb rapidjson ];
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cmakeFlags = [
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"-DPORTABLE=off"
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"-DRAPIDJSON_HOME=${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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# Fix gcc-13 build by adding missing <cstdint> includes:
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# https://github.com/sortmerna/sortmerna/issues/412
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sed -e '1i #include <cstdint>' -i include/kseq_load.hpp
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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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mainProgram = "sortmerna";
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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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broken = stdenv.isDarwin;
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};
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}
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