diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix new file mode 100644 index 00000000000..05cd7992aa9 --- /dev/null +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -0,0 +1,42 @@ +{stdenv, fetchFromGitHub, nim, htslib, patchelf, pcre}: + +let + hts-nim = fetchFromGitHub { + owner = "brentp"; + repo = "hts-nim"; + rev = "9cd83e30522ab64cd71eb8209be4154aa5579ce1"; + sha256 = "10g408idy14667varq1syf06rrbpk63i3ib7i5dh1md4ib19av6f"; + }; + + docopt = fetchFromGitHub { + owner = "docopt"; + repo = "docopt.nim"; + rev = "v0.6.5"; + sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr"; + }; + +in stdenv.mkDerivation rec { + name = "mosdepth-${version}"; + version = "0.2.3"; + + src = fetchFromGitHub { + owner = "brentp"; + repo = "mosdepth"; + rev = "v${version}"; + sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7"; + }; + + buildInputs = [ nim ]; + + buildPhase = "nim -p:${hts-nim}/src -p:${docopt}/src c -d:release mosdepth.nim"; + installPhase = "install -Dt $out/bin mosdepth"; + fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth"; + + meta = with stdenv.lib; { + description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing."; + license = licenses.mit; + homepage = https://github.com/brentp/mosdepth; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 41f79a08b3f..1dd86617935 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20255,6 +20255,8 @@ with pkgs; minimap2 = callPackage ../applications/science/biology/minimap2 { }; + mosdepth = callPackage ../applications/science/biology/mosdepth { }; + ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { }; paml = callPackage ../applications/science/biology/paml { };