646b892680
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71 lines
1.8 KiB
Nix
71 lines
1.8 KiB
Nix
{
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lib,
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stdenv,
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fetchFromGitHub,
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cmake,
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perl,
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python3,
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onetbb,
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zlib,
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runCommand,
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bowtie2,
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "bowtie2";
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version = "2.5.4";
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src = fetchFromGitHub {
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owner = "BenLangmead";
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repo = "bowtie2";
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tag = "v${finalAttrs.version}";
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fetchSubmodules = true;
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hash = "sha256-ZbmVOItfAgKdsMrvQIXgKiPtoQJZYfGblCGDoNPjvTU=";
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};
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# because of this flag, gcc on aarch64 cannot find the Threads
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# Could NOT find Threads (missing: Threads_FOUND)
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# TODO: check with other distros and report upstream
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postPatch = ''
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substituteInPlace CMakeLists.txt \
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--replace "-m64" ""
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'';
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nativeBuildInputs = [ cmake ];
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buildInputs = [
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onetbb
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zlib
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python3
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perl
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];
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cmakeFlags = lib.optional (!stdenv.hostPlatform.isx86) [
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"-DCMAKE_CXX_FLAGS=-I${finalAttrs.src}/third_party"
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];
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# ctest fails because of missing dependencies between tests
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doCheck = false;
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passthru.tests = {
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ctest = runCommand "${finalAttrs.pname}-test" { } ''
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mkdir $out
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${lib.getExe bowtie2} -x ${finalAttrs.src}/example/index/lambda_virus ${finalAttrs.src}/example/reads/longreads.fq -u 10
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${bowtie2}/bin/bowtie2-build-s -c GGGCGGCGACCTCGCGGGTTTTCGCTA $out/small
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${bowtie2}/bin/bowtie2-inspect-s $out/small
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${bowtie2}/bin/bowtie2-build-l -c GGGCGGCGACCTCGCGGGTTTTCGCTA $out/large
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${bowtie2}/bin/bowtie2-inspect-l $out/large
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'';
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};
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meta = with lib; {
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description = "Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
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license = licenses.gpl3Plus;
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homepage = "http://bowtie-bio.sf.net/bowtie2";
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changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/v${finalAttrs.version}";
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maintainers = with maintainers; [ rybern ];
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platforms = platforms.all;
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mainProgram = "bowtie2";
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};
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})
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