Merge pull request #93429 from danieldk/sortmerna-4.2.0

sortmerna: 3.0.3 -> 4.2.0

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;