grenedalf: init at 0.6.2 (#366618)

2025-03-12 16:34:59 +01:00
parent 917d5fc5f1 261feca650
commit 64bd798e0f
1 changed files with 85 additions and 0 deletions
@@ -0,0 +1,85 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  autoconf,
+  pkg-config,
+  libz,
+  bzip2,
+  xz,
+  libdeflate,
+  htslib,
+  fetchurl,
+}:
+
+let
+  # Grenedalf is binded to htslib 1.16 and does not link with libcurl
+  htslib_gr = htslib.overrideDerivation (oldAttrs: rec {
+    version = "1.16";
+    name = "${oldAttrs.pname}-nocurl-${version}";
+    src = fetchurl {
+      url = "https://github.com/samtools/htslib/releases/download/${version}/htslib-${version}.tar.bz2";
+      sha256 = "sha256-YGt8ev9zc0zwM+zRVvQFKfpXkvVFJJUqKJOMoIkNeSQ=";
+    };
+    configureFlags = [
+      "--disable-libcurl"
+      "--disable-plugins"
+    ];
+  });
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "grenedalf";
+  version = "0.6.2";
+
+  src = fetchFromGitHub {
+    owner = "lczech";
+    repo = "grenedalf";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-DJ7nZjOvYFQlN/L+S2QcMVvH/M9Dhla4VXl2nxc22m4=";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    autoconf
+  ];
+
+  buildInputs = [
+    libz
+    bzip2
+    xz
+    libdeflate
+    htslib_gr
+  ];
+
+  cmakeFlags = [
+    "-DHTSLIB_DIR=${htslib_gr}"
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp ../bin/grenedalf $out/bin
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/lczech/grenedalf";
+    description = "Collection of commands for working with population genetic data";
+    longDescription = ''
+      grenedalf is a collection of commands for working with population genetic
+      data, in particular from pool sequencing. Its main focus are statistical
+      analyses such as Tajima's D and Fst. The statistics follow the approaches
+      of PoPoolation and PoPoolation2, as well as poolfstat and npstat. However,
+      compared to those, grenedalf is significantly more scalable, more user
+      friendly, and offers more settings and input file formats.
+    '';
+    platforms = platforms.all;
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ bzizou ];
+  };
+})