56 lines
2.1 KiB
Nix
56 lines
2.1 KiB
Nix
{ lib, stdenv, zlib, bzip2, xz, fetchFromGitHub } :
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stdenv.mkDerivation rec {
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version = "1.1.0";
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pname = "svaba";
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src = fetchFromGitHub {
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owner = "walaj";
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repo = pname;
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rev = version;
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sha256 = "1vv5mc9z5d22kgdy7mm27ya5aahnqgkcrskdr2405058ikk9g8kp";
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fetchSubmodules = true;
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};
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buildInputs = [ zlib bzip2 xz ];
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postPatch = ''
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# Fix gcc-13 build failure due to missing includes
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sed -e '1i #include <cstdint>' -i \
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SeqLib/src/non_api/Histogram.h \
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src/svaba/Histogram.h
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'';
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# Workaround build failure on -fno-common toolchains like upstream
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# gcc-10. Otherwise build fails as:
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# ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of
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# `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here
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env.NIX_CFLAGS_COMPILE = "-fcommon";
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installPhase = ''
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runHook preInstall
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install -Dm555 src/svaba/svaba $out/bin/svaba
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runHook postInstall
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'';
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meta = with lib; {
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broken = (stdenv.isLinux && stdenv.isAarch64);
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description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly";
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license = licenses.gpl3;
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homepage = "https://github.com/walaj/svaba";
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maintainers = with maintainers; [ scalavision ];
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platforms = platforms.linux;
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longDescription = ''
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SvABA is a method for detecting structural variants in sequencing data
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using genome-wide local assembly. Under the hood, SvABA uses a custom
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implementation of SGA (String Graph Assembler) by Jared Simpson,
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and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window
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(with some small overlap) for every region in the genome.
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The default is to use only clipped, discordant, unmapped and indel reads,
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although this can be customized to any set of reads at the command line using VariantBam rules.
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These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants.
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Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.
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'';
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};
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}
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