SPAdes: refactor

NixOS · Jun 16, 2024 · 63b875e · 63b875e
1 parent 80f3f19
commit 63b875e
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Showing 4 changed files with 47 additions and 34 deletions.
diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix
diff --git a/pkgs/by-name/sp/spades/package.nix b/pkgs/by-name/sp/spades/package.nix
@@ -0,0 +1,46 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  zlib,
+  bzip2,
+  cmake,
+  python3,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "spades";
+  version = "3.15.5";
+
+  src = fetchurl {
+    url = "https://github.com/ablab/spades/releases/download/v${finalAttrs.version}/SPAdes-${finalAttrs.version}.tar.gz";
+    hash = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";
+  };
+  sourceRoot = "SPAdes-${finalAttrs.version}/src";
+
+  env.CXXFLAGS = toString [
+    # GCC 13: error: 'uint32_t' does not name a type
+    "-include cstdint"
+  ];
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [
+    zlib
+    bzip2
+    python3
+  ];
+
+  doCheck = true;
+
+  meta = {
+    description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data";
+    license = lib.licenses.gpl2Only;
+    homepage = "http://ablab.github.io/spades";
+    platforms = [
+      "x86_64-linux"
+      "x86_64-darwin"
+    ];
+    maintainers = with lib.maintainers; [ bzizou ];
+  };
+})
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
@@ -1228,6 +1228,7 @@ mapAliases ({
   solr = throw "'solr' has been removed from nixpkgs, as it was broken and unmaintained"; # Added 2023-03-16
   soundOfSorting = sound-of-sorting; # Added 2023-07-07
   soundux = throw "'soundux' has been removed, as it is unmaintained."; # Added on 2024-02-14
+  SPAdes = spades; # Added 2024-06-12
   spark2 = throw "'spark2' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08
   spark_2_4 = throw "'spark_2_4' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08
   spark_3_1 = throw "'spark_3_1' is no longer supported nixpkgs, please use 'spark'"; # Added 2023-05-08

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
@@ -37945,8 +37945,6 @@ with pkgs;
 
   seaview = callPackage ../applications/science/biology/seaview { };
 
-  SPAdes = callPackage ../applications/science/biology/spades { };
-
   svaba = callPackage ../applications/science/biology/svaba { };
 
   tandem-aligner = callPackage ../applications/science/biology/tandem-aligner { };