73 lines
1.6 KiB
Nix
73 lines
1.6 KiB
Nix
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{
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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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concurrentqueue = fetchFromGitHub {
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owner = "cameron314";
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repo = "concurrentqueue";
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tag = "v1.0.4";
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hash = "sha256-MkhlDme6ZwKPuRINhfpv7cxliI2GU3RmTfC6O0ke/IQ=";
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};
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in
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stdenv.mkDerivation rec {
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pname = "sortmerna";
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version = "4.3.7";
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src = fetchFromGitHub {
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owner = "sortmerna";
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repo = "sortmerna";
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tag = "v${version}";
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hash = "sha256-oxwZBkeW3usEcJE1XLu1UigKsgOsljwGFTpb7U3845I=";
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};
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nativeBuildInputs = [
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cmake
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pkg-config
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];
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buildInputs = [
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zlib
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rocksdb
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rapidjson
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];
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cmakeFlags = [
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"-DPORTABLE=off"
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"-DRAPIDJSON_HOME=${rapidjson}"
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"-DROCKSDB_HOME=${rocksdb}"
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"-DCONCURRENTQUEUE_HOME=${concurrentqueue}"
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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 missing pthread dependency for the main binary.
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substituteInPlace src/sortmerna/CMakeLists.txt \
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--replace-fail "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 = {
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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 = lib.licenses.lgpl3;
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platforms = lib.platforms.x86_64;
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homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
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maintainers = with lib.maintainers; [ luispedro ];
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broken = stdenv.hostPlatform.isDarwin;
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};
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}
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