From 661048c803f7c0c7aa1915162580b7c21316a4a3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 7 Mar 2017 15:46:53 +1100
Subject: [PATCH] platypus: init at 2017-03-07

---
 .../science/biology/platypus/default.nix      | 38 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 40 insertions(+)
 create mode 100644 pkgs/applications/science/biology/platypus/default.nix

diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix
new file mode 100644
index 000000000000..868540fcbc3b
--- /dev/null
+++ b/pkgs/applications/science/biology/platypus/default.nix
@@ -0,0 +1,38 @@
+{stdenv, fetchFromGitHub, python27, htslib, zlib, makeWrapper}:
+
+let python = python27.withPackages (ps: with ps; [ cython ]);
+
+in stdenv.mkDerivation rec {
+  name = "platypus-unstable-${version}";
+  version = "2017-03-07";
+
+  src = fetchFromGitHub {
+    owner = "andyrimmer";
+    repo = "Platypus";
+    rev = "cbbd914";
+    sha256 = "0xgj3pl7n4c12j5pp5qyjfk4rsvb5inwzrpcbhdf3br5f3mmdsb9";
+  };
+
+  buildInputs = [ htslib python zlib makeWrapper ];
+
+  buildPhase = ''
+    patchShebangs .
+    make
+  '';
+
+  installPhase = ''
+    mkdir -p $out/libexec/platypus
+    cp -r ./* $out/libexec/platypus
+
+    mkdir -p $out/bin
+    makeWrapper ${python}/bin/python $out/bin/platypus --add-flags "$out/libexec/platypus/bin/Platypus.py"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "The Platypus variant caller";
+    license = licenses.gpl3;
+    homepage = https://github.com/andyrimmer/Platypus;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 3ab8684bec25..12d9b13bc781 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16996,6 +16996,8 @@ with pkgs;
 
   paml = callPackage ../applications/science/biology/paml { };
 
+  platypus = callPackage ../applications/science/biology/platypus/default.nix { };
+
   plink = callPackage ../applications/science/biology/plink/default.nix { };
 
   plink-ng = callPackage ../applications/science/biology/plink-ng/default.nix { };