1 files changed, 46 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..715f2ea313b4
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -0,0 +1,46 @@
+{lib, stdenv, fetchFromGitHub, nim, htslib, pcre}:
+
+let
+  hts-nim = fetchFromGitHub {
+    owner = "brentp";
+    repo = "hts-nim";
+    rev = "v0.3.4";
+    sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
+  };
+
+  docopt = fetchFromGitHub {
+    owner = "docopt";
+    repo = "docopt.nim";
+    rev = "v0.6.7";
+    sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
+  };
+
+in stdenv.mkDerivation rec {
+  pname = "mosdepth";
+  version = "0.3.2";
+
+  src = fetchFromGitHub {
+    owner = "brentp";
+    repo = "mosdepth";
+    rev = "v${version}";
+    sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ=";
+  };
+
+  nativeBuildInputs = [ nim ];
+  buildInputs = [ htslib pcre ];
+
+  buildPhase = ''
+    HOME=$TMPDIR
+    nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim
+  '';
+
+  installPhase = "install -Dt $out/bin mosdepth";
+
+  meta = with 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;
+  };
+}