70 lines
1.8 KiB
Nix
70 lines
1.8 KiB
Nix
{ lib
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, stdenv
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, fetchFromGitHub
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, boost
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, bzip2
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, htslib
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, llvmPackages
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, xz
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, zlib
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, delly
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, runCommand
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "delly";
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version = "1.2.6";
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src = fetchFromGitHub {
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owner = "dellytools";
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repo = "delly";
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rev = "v${finalAttrs.version}";
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hash = "sha256-OO5nnaIcfNAV8pc03Z8YS5kE96bFOrJXA9QTiLi7vPc=";
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};
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buildInputs = [
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boost
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bzip2
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htslib
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xz
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zlib
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] ++ lib.optional stdenv.isDarwin llvmPackages.openmp;
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makeFlags = [
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"EBROOTHTSLIB=${htslib}"
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"PARALLEL=1"
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];
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installPhase = ''
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runHook preInstall
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install -Dm555 src/delly $out/bin/delly
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runHook postInstall
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'';
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passthru.tests = {
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simple = runCommand "${finalAttrs.pname}-test" { } ''
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mkdir $out
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${lib.getExe delly} call -g ${delly.src}/example/ref.fa ${delly.src}/example/sr.bam > $out/sr.vcf
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${lib.getExe delly} lr -g ${delly.src}/example/ref.fa ${delly.src}/example/lr.bam > $out/lr.vcf
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${lib.getExe delly} cnv -g ${delly.src}/example/ref.fa -m ${delly.src}/example/map.fa.gz ${delly.src}/example/sr.bam > cnv.vcf
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'';
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};
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meta = with lib; {
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description = "Structural variant caller for mapped DNA sequenced data";
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mainProgram = "delly";
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license = licenses.bsd3;
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maintainers = with maintainers; [ scalavision ];
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platforms = platforms.unix;
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longDescription = ''
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Delly is an integrated structural variant (SV) prediction method
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that can discover, genotype and visualize deletions, tandem duplications,
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inversions and translocations at single-nucleotide resolution in
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short-read massively parallel sequencing data. It uses paired-ends,
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split-reads and read-depth to sensitively and accurately delineate
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genomic rearrangements throughout the genome.
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'';
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};
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})
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