Merge pull request #320502 from bzizou/spades4

spades: 3.15.5 -> 4.0.0

pkgs/by-name/sp/spades/package.nix

@@ -1,46 +1,74 @@
 {
   lib,
   stdenv,
-  fetchurl,
-  zlib,
   bzip2,
   cmake,
+  fetchFromGitHub,
+  fetchpatch,
+  ncurses,
   python3,
+  readline,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "spades";
-  version = "3.15.5";
+  version = "4.0.0";
 
-  src = fetchurl {
-    url = "https://github.com/ablab/spades/releases/download/v${finalAttrs.version}/SPAdes-${finalAttrs.version}.tar.gz";
-    hash = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";
+  src = fetchFromGitHub {
+    owner = "ablab";
+    repo = "spades";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-k2+ddJIgGE41KGZODovU9VdurbWerEtdqNrFDwyuFjo=";
   };
-  sourceRoot = "SPAdes-${finalAttrs.version}/src";
 
-  env.CXXFLAGS = toString [
-    # GCC 13: error: 'uint32_t' does not name a type
-    "-include cstdint"
+  sourceRoot = "source/src";
+
+  patches = [
+    # https://github.com/ablab/spades/pull/1314
+    (fetchpatch {
+      name = "copytree.patch";
+      url = "https://github.com/ablab/spades/commit/af1f756a46c5da669897b841d4f753af1eaa9588.patch";
+      hash = "sha256-tkT7hb0TqsbLkcTs9u43nzvV8bVdh3G9VKYqFFLrQv8=";
+      stripLen = 3;
+      extraPrefix = "projects/";
+    })
   ];
 
+  cmakeFlags = [
+    "-DZLIB_ENABLE_TESTS=OFF"
+    "-DSPADES_BUILD_INTERNAL=OFF"
+  ];
+
+  preConfigure = ''
+    # The CMakeListsInternal.txt file should be empty in the release tarball
+    echo "" > CMakeListsInternal.txt
+  '';
+
   nativeBuildInputs = [ cmake ];
 
   buildInputs = [
-    zlib
     bzip2
+    ncurses
     python3
+    readline
   ];
 
   doCheck = true;
 
+  strictDeps = true;
+
   meta = {
     description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data";
-    license = lib.licenses.gpl2Only;
+    changelog = "https://github.com/ablab/spades/blob/${finalAttrs.version}/changelog.md";
+    downloadPage = "https://github.com/ablab/spades";
     homepage = "http://ablab.github.io/spades";
+    license = lib.licenses.gpl2Only;
     platforms = [
+      "aarch64-linux"
       "x86_64-linux"
       "x86_64-darwin"
     ];
     maintainers = with lib.maintainers; [ bzizou ];
+    broken = stdenv.hostPlatform.isMusl;
   };
 })