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