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{ pkgs, stdenv, fetchFromGitHub, boost, zlib, lib, makeWrapper }:
let
# Bcftools needs perl
runtime = with pkgs; [ bcftools htslib my-python perl samtools ];
my-python-packages = p: with p; [
bx-python
pysam
cython
pandas
psutil
nose
scipy
];
my-python = pkgs.python3.withPackages my-python-packages;
in
stdenv.mkDerivation rec {
pname = "hap.py";
version = "0.3.15";
src = fetchFromGitHub {
owner = "Illumina";
repo = pname;
rev = "v${version}";
sha256 = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";
};
# For illumina script
BOOST_ROOT = "${boost.out}";
ZLIBSTATIC = "${zlib.static}";
# For cmake : boost lib and includedir are in differernt location
BOOST_LIBRARYDIR = "${boost.out}/lib";
BOOST_INCLUDEDIR = "${boost.dev}/include";
patches = [
./hap-py.patch
./cmake.patch
];
buildInputs = with pkgs; [
autoconf
boost
bzip2
cmake
curl
htslib
my-python
xz
zlib
];
nativeBuildInputs = [ pkgs.makeWrapper ];
propagatedBuildInputs = runtime;
postFixup = ''
wrapProgram $out/bin/hap.py \
--set PATH ${lib.makeBinPath runtime}
'';
meta = with lib; {
description = "Compare genetics variants against a gold dataset";
homepage = "https://github.com/Illumina/hap.py";
license = licenses.bsd2;
maintainers = with maintainers; [ apraga ];
mainProgram = "hap.py";
};
}
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