sortmerna: 4.2.0 -> 4.3.7

NixOS · Mar 1, 2025 · b5e0951 · b5e0951
1 parent 0823e91
commit b5e0951
Showing 1 changed file with 18 additions and 15 deletions.
diff --git a/pkgs/by-name/so/sortmerna/package.nix b/pkgs/by-name/so/sortmerna/package.nix
@@ -11,22 +11,29 @@
 
 let
   rocksdb = rocksdb_8_3;
+  concurrentqueue = fetchFromGitHub {
+    owner = "cameron314";
+    repo = "concurrentqueue";
+    tag = "v1.0.4";
+    hash = "sha256-MkhlDme6ZwKPuRINhfpv7cxliI2GU3RmTfC6O0ke/IQ=";
+  };
 in
 stdenv.mkDerivation rec {
   pname = "sortmerna";
-  version = "4.2.0";
+  version = "4.3.7";
 
   src = fetchFromGitHub {
-    repo = pname;
-    owner = "biocore";
-    rev = "v${version}";
-    sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
+    owner = "sortmerna";
+    repo = "sortmerna";
+    tag = "v${version}";
+    hash = "sha256-oxwZBkeW3usEcJE1XLu1UigKsgOsljwGFTpb7U3845I=";
   };
 
   nativeBuildInputs = [
     cmake
     pkg-config
   ];
+
   buildInputs = [
     zlib
     rocksdb
@@ -37,33 +44,29 @@ stdenv.mkDerivation rec {
     "-DPORTABLE=off"
     "-DRAPIDJSON_HOME=${rapidjson}"
     "-DROCKSDB_HOME=${rocksdb}"
+    "-DCONCURRENTQUEUE_HOME=${concurrentqueue}"
     "-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" \
+      --replace-fail "target_link_libraries(sortmerna" \
         "target_link_libraries(sortmerna Threads::Threads"
 
     # Fix gcc-13 build by adding missing <cstdint> includes:
     #   https://github.com/sortmerna/sortmerna/issues/412
     sed -e '1i #include <cstdint>' -i include/kseq_load.hpp
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
     mainProgram = "sortmerna";
-    license = licenses.lgpl3;
-    platforms = platforms.x86_64;
+    license = lib.licenses.lgpl3;
+    platforms = lib.platforms.x86_64;
     homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/";
-    maintainers = with maintainers; [ luispedro ];
+    maintainers = with lib.maintainers; [ luispedro ];
     broken = stdenv.hostPlatform.isDarwin;
   };
 }