1 files changed, 45 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
new file mode 100644
index 000000000000..3cd83a5cdd27
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -0,0 +1,45 @@
+{stdenv, fetchFromGitHub, nim, htslib, pcre}:
+
+let
+  hts-nim = fetchFromGitHub {
+    owner = "brentp";
+    repo = "hts-nim";
+    rev = "v0.2.5";
+    sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb";
+  };
+
+  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 = ''
+    HOME=$TMPDIR
+    nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -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;
+  };
+}