2019-12-17 22:37:39 +00:00
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{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
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, samtools, hexdump, python2Packages, which }:
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let
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python =
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python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
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in stdenv.mkDerivation rec {
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pname = "lumpy";
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2020-10-29 12:27:45 +00:00
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version = "0.3.1";
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2019-12-17 22:37:39 +00:00
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src = fetchFromGitHub {
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owner = "arq5x";
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repo = "lumpy-sv";
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2020-10-29 12:27:45 +00:00
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rev = "v${version}";
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sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
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fetchSubmodules = true;
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2019-12-17 22:37:39 +00:00
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};
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nativeBuildInputs = [ which ];
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buildInputs =
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[ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
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preConfigure = ''
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patchShebangs ./.
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# Use Nix htslib over bundled version
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sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
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sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
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2020-10-29 12:27:45 +00:00
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# Also make sure we use the includes from Nix's htslib
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sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
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2019-12-17 22:37:39 +00:00
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'';
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# Upstream's makefile doesn't have an install target
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installPhase = ''
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mkdir -p $out
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cp -r bin $out
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cp -r scripts $out
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sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
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'';
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meta = with stdenv.lib; {
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description = "Probabilistic structural variant caller";
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homepage = "https://github.com/arq5x/lumpy-sv";
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maintainers = with maintainers; [ jbedo ];
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license = licenses.mit;
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platforms = [ "x86_64-linux" ];
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};
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}
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