1 files changed, 102 insertions, 0 deletions
diff --git a/pkgs/by-name/ab/abpoa/package.nix b/pkgs/by-name/ab/abpoa/package.nix
new file mode 100644
index 0000000000000..7641674e61b1a
--- /dev/null
+++ b/pkgs/by-name/ab/abpoa/package.nix
@@ -0,0 +1,102 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  simde,
+  zlib,
+  enableSse4_1 ? stdenv.hostPlatform.sse4_1Support,
+  enableAvx ? stdenv.hostPlatform.avxSupport,
+  enablePython ? false,
+  python3Packages,
+  runCommand,
+  abpoa,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "${lib.optionalString enablePython "py"}abpoa";
+  version = "1.5.2";
+
+  src = fetchFromGitHub {
+    owner = "yangao07";
+    repo = "abPOA";
+    rev = "refs/tags/v${finalAttrs.version}";
+    hash = "sha256-gS0PO7K4hN+3k2NF8enri1FzM80H2I+a3MNaKsm74xM=";
+  };
+
+  patches = [ ./simd-arch.patch ];
+
+  postPatch = ''
+    cp -r ${simde.src}/* include/simde
+    substituteInPlace Makefile \
+      --replace-fail "-march=native" ""
+  '';
+
+  nativeBuildInputs = lib.optionals enablePython (
+    with python3Packages;
+    [
+      cython_0
+      pypaBuildHook
+      pypaInstallHook
+      pythonImportsCheckHook
+      setuptools
+    ]
+  );
+
+  buildFlags = lib.optionals stdenv.hostPlatform.isx86_64 [
+    (
+      if enableAvx then
+        "avx2=1"
+      else if enableSse4_1 then
+        "sse41=1"
+      else
+        "sse2=1"
+    )
+  ];
+
+  env = lib.optionalAttrs enablePython (
+    if enableAvx then
+      { "AVX2" = 1; }
+    else if enableSse4_1 then
+      { "SSE41" = 1; }
+    else
+      { "SSE2" = 1; }
+  );
+
+  buildInputs = [ zlib ];
+
+  installPhase = lib.optionalString (!enablePython) ''
+    runHook preInstall
+
+    install -Dm755 ./bin/abpoa -t $out/bin
+
+    runHook postInstall
+  '';
+
+  pythonImportsCheck = [ "pyabpoa" ];
+
+  doInstallCheck = enablePython;
+
+  installCheckPhase = ''
+    runHook preInstallCheck
+
+    python python/example.py
+
+    runHook postInstallCheck
+  '';
+
+  passthru.tests = {
+    simple = runCommand "${finalAttrs.pname}-test" { } ''
+      ${lib.getExe abpoa} ${abpoa.src}/test_data/seq.fa > $out
+    '';
+  };
+
+  meta = with lib; {
+    description = "SIMD-based C library for fast partial order alignment using adaptive band";
+    homepage = "https://github.com/yangao07/abPOA";
+    changelog = "https://github.com/yangao07/abPOA/releases/tag/${finalAttrs.src.rev}";
+    license = licenses.mit;
+    maintainers = with maintainers; [ natsukium ];
+    mainProgram = "abpoa";
+    platforms = platforms.unix;
+  };
+})