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|
{ lib
, stdenv
, fetchFromGitHub
, boost
, bzip2
, htslib
, llvmPackages
, xz
, zlib
, delly
, runCommand
}:
stdenv.mkDerivation (finalAttrs: {
pname = "delly";
version = "1.1.8";
src = fetchFromGitHub {
owner = "dellytools";
repo = "delly";
rev = "v${finalAttrs.version}";
hash = "sha256-IxZPbcM52E1bzy6msGmka6Ykgc+OLWTMhWBCn0E4mFI=";
};
buildInputs = [
boost
bzip2
htslib
xz
zlib
] ++ lib.optional stdenv.isDarwin llvmPackages.openmp;
makeFlags = [
"EBROOTHTSLIB=${htslib}"
"PARALLEL=1"
];
installPhase = ''
runHook preInstall
install -Dm555 src/delly $out/bin/delly
runHook postInstall
'';
passthru.tests = {
simple = runCommand "${finalAttrs.pname}-test" { } ''
mkdir $out
${lib.getExe delly} call -g ${delly.src}/example/ref.fa ${delly.src}/example/sr.bam > $out/sr.vcf
${lib.getExe delly} lr -g ${delly.src}/example/ref.fa ${delly.src}/example/lr.bam > $out/lr.vcf
${lib.getExe delly} cnv -g ${delly.src}/example/ref.fa -m ${delly.src}/example/map.fa.gz ${delly.src}/example/sr.bam > cnv.vcf
'';
};
meta = with lib; {
description = "Structural variant caller for mapped DNA sequenced data";
license = licenses.bsd3;
maintainers = with maintainers; [ scalavision ];
platforms = platforms.unix;
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.
'';
};
})
|