1 files changed, 35 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
new file mode 100644
index 000000000000..c4b4bb522c40
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix
@@ -0,0 +1,35 @@
+{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "samtools";
+  version = "1.9";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8";
+  };
+
+  nativeBuildInputs = [ perl ];
+
+  buildInputs = [ zlib ncurses htslib ];
+
+  configureFlags = [ "--with-htslib=${htslib}" ]
+    ++ stdenv.lib.optional (ncurses == null) "--without-curses";
+
+  preCheck = ''
+    patchShebangs test/
+  '';
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    description = "Tools for manipulating SAM/BAM/CRAM format";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}