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{ stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
let
htslibPatch = fetchpatch {
url = "https://github.com/dellytools/delly/commit/0e5c710b0c5ea790bb39699d4cbd49cf4fb86f14.diff";
sha256 = "09bz1qqvzhdzm99hf9zgrv80kq9jlr1m2mdvx96p2hk5lpnbdl7y";
excludes = [ "src/htslib" ];
};
in stdenv.mkDerivation rec {
pname = "delly";
version = "0.8.2";
src = fetchFromGitHub {
owner = "dellytools";
repo = pname;
rev = "v${version}";
sha256 = "14bkmixz7737xj192ww96s3a20zc7xs7r04db8avw3ggi3i1s1cs";
};
patches = [ htslibPatch ];
buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
EBROOTHTSLIB = htslib;
installPhase = ''
runHook preInstall
install -Dm555 src/delly $out/bin/delly
runHook postInstall
'';
meta = with stdenv.lib; {
description = "Structural variant caller for mapped DNA sequenced data";
license = licenses.gpl3;
maintainers = with maintainers; [ scalavision ];
platforms = platforms.linux;
longDescription = ''
Delly is an integrated structural variant (SV) prediction method
that can discover, genotype and visualize deletions, tandem duplications,
inversions and translocations at single-nucleotide resolution in
short-read massively parallel sequencing data. It uses paired-ends,
split-reads and read-depth to sensitively and accurately delineate
genomic rearrangements throughout the genome.
'';
};
}
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