Merge pull request #43096 from jbedo/mosdepth

mosdepth: init 0.2.3

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;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -20264,6 +20264,8 @@ 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 { };