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571c71e6f7
We are migrating packages that meet below requirements:
1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration
The tool is here: https://github.com/Aleksanaa/by-name-migrate.
63 lines
1.8 KiB
Nix
63 lines
1.8 KiB
Nix
{ 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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, tbb
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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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rev = "refs/tags/v${finalAttrs.version}";
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fetchSubmodules = true;
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hash = "sha256-ZbmVOItfAgKdsMrvQIXgKiPtoQJZYfGblCGDoNPjvTU=";
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};
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# because of this flag, gcc on aarch64 cannot find the Threads
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# Could NOT find Threads (missing: Threads_FOUND)
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# TODO: check with other distros and report upstream
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postPatch = ''
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substituteInPlace CMakeLists.txt \
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--replace "-m64" ""
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'';
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nativeBuildInputs = [ cmake ];
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buildInputs = [ tbb zlib python3 perl ];
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cmakeFlags = lib.optional (!stdenv.hostPlatform.isx86) ["-DCMAKE_CXX_FLAGS=-I${finalAttrs.src}/third_party"];
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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 $out/large
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'';
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};
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meta = with lib; {
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description = "Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
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license = licenses.gpl3Plus;
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homepage = "http://bowtie-bio.sf.net/bowtie2";
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changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}";
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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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