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{ lib, stdenv, cmake, rocksdb, rapidjson, pkg-config, fetchFromGitHub, zlib }:
stdenv.mkDerivation rec {
pname = "sortmerna";
version = "4.2.0";
src = fetchFromGitHub {
repo = pname;
owner = "biocore";
rev = "v${version}";
sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
};
nativeBuildInputs = [ cmake pkg-config ];
buildInputs = [ zlib rocksdb rapidjson ];
cmakeFlags = [
"-DCMAKE_BUILD_TYPE=Release"
"-DPORTABLE=off"
"-DRAPIDJSON_HOME=${rapidjson}"
"-DROCKSDB_HOME=${rocksdb}"
"-DROCKSDB_STATIC=off"
"-DZLIB_STATIC=off"
];
postPatch = ''
# Fix formatting string error:
# https://github.com/biocore/sortmerna/issues/255
substituteInPlace src/sortmerna/indexdb.cpp \
--replace 'is_verbose, ss' 'is_verbose, "%s", ss'
# Fix missing pthread dependency for the main binary.
substituteInPlace src/sortmerna/CMakeLists.txt \
--replace "target_link_libraries(sortmerna" \
"target_link_libraries(sortmerna Threads::Threads"
'';
meta = with lib; {
description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
license = licenses.lgpl3;
platforms = platforms.x86_64;
homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
maintainers = with maintainers; [ luispedro ];
broken = stdenv.isDarwin;
};
}
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