Merge pull request #248172 from alxsimon/bwa

bwa-mem2: init at version 2.2.1

pkgs/applications/science/biology/bwa-mem2/default.nix

···
+{ lib
+, stdenv
+, fetchFromGitHub
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "bwa-mem2";
+  version = "unstable-2023-03-18";
+
+  src = fetchFromGitHub {
+    owner = "bwa-mem2";
+    repo = "bwa-mem2";
+    rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
+    fetchSubmodules = true;
+    hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
+  };
+
+  buildInputs = [ zlib ];
+
+  # see https://github.com/bwa-mem2/bwa-mem2/issues/93
+  postPatch = lib.optionalString stdenv.isDarwin ''
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
+    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
+  '';
+
+  buildFlags = [
+    (if stdenv.hostPlatform.sse4_2Support then "arch=sse42"
+    else if stdenv.hostPlatform.avxSupport then "arch=avx"
+    else if stdenv.hostPlatform.avx2Support then "arch=avx2"
+    else if stdenv.hostPlatform.avx512Support then "arch=avx512"
+    else "arch=sse41")
+  ];
+  enableParallelBuilding = true;
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp bwa-mem2* $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome";
+    license = licenses.mit;
+    homepage = "https://github.com/bwa-mem2/bwa-mem2/";
+    changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md";
+    platforms = platforms.x86_64;
+    maintainers = with maintainers; [ alxsimon ];
+  };
+})

pkgs/top-level/all-packages.nix

···
 
   bwa = callPackage ../applications/science/biology/bwa { };
 
+  bwa-mem2 = callPackage ../applications/science/biology/bwa-mem2 { };
+
   ### SCIENCE/MACHINE LEARNING
 
   nengo-gui = callPackage ../applications/science/machine-learning/nengo-gui { };