commit 8e2c3b93bae2d0bcc020f93ed0dcdb7a206eaf52 · pyrox.dev/nixpkgs

+42

pkgs/applications/science/biology/mosdepth/default.nix

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       {stdenv, fetchFromGitHub, nim, htslib, patchelf, pcre}:

     

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       let

     

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         hts-nim = fetchFromGitHub {

     

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           owner = "brentp";

     

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           repo = "hts-nim";

     

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           rev = "9cd83e30522ab64cd71eb8209be4154aa5579ce1";

     

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           sha256 = "10g408idy14667varq1syf06rrbpk63i3ib7i5dh1md4ib19av6f";

     

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         };

     

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         docopt = fetchFromGitHub {

     

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           owner = "docopt";

     

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           repo = "docopt.nim";

     

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           rev = "v0.6.5";

     

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           sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr";

     

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         };

     

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       in stdenv.mkDerivation rec {

     

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         name = "mosdepth-${version}";

     

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         version = "0.2.3";

     

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         src = fetchFromGitHub {

     

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           owner = "brentp";

     

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           repo = "mosdepth";

     

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           rev = "v${version}";

     

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           sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7";

     

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         };

     

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         buildInputs = [ nim ];

     

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         buildPhase = "nim -p:${hts-nim}/src -p:${docopt}/src c -d:release mosdepth.nim";

     

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         installPhase = "install -Dt $out/bin mosdepth";

     

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         fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth";

     

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         meta = with stdenv.lib; {

     

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           description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.";

     

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           license = licenses.mit;

     

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           homepage = https://github.com/brentp/mosdepth;

     

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           maintainers = with maintainers; [ jbedo ];

     

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           platforms = platforms.linux;

     

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         };

     

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       }

pkgs/top-level/all-packages.nix

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         minimap2 = callPackage ../applications/science/biology/minimap2 { };

     

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         mosdepth = callPackage ../applications/science/biology/mosdepth { };

     

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         ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { };

     

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         paml = callPackage ../applications/science/biology/paml { };