diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index 1f291d1a700..4e32669dfca 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -2,32 +2,39 @@ stdenv.mkDerivation rec { pname = "sortmerna"; - version = "3.0.3"; + version = "4.2.0"; src = fetchFromGitHub { repo = pname; owner = "biocore"; rev = "v${version}"; - sha256 = "0zx5fbzyr8wdr0zwphp8hhcn1xz43s5lg2ag4py5sv0pv5l1jh76"; + sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j"; }; - patches = [ - (fetchpatch { - name = "CMakeInstallPrefix.patch"; - url = "https://github.com/biocore/sortmerna/commit/4d36d620a3207e26cf3f588d4ec39889ea21eb79.patch"; - sha256 = "0hc3jwdr6ylbyigg52q8islqc0mb1k8rrjadvjfqaxnili099apd"; - }) - ]; - - nativeBuildInputs = [ cmake rapidjson pkgconfig ]; + nativeBuildInputs = [ cmake pkgconfig ]; buildInputs = [ zlib rocksdb rapidjson ]; cmakeFlags = [ "-DCMAKE_BUILD_TYPE=Release" - "-DROCKSDB_HOME=${rocksdb}" + "-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 stdenv.lib; { description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; license = licenses.lgpl3;