From a6d6a3972f22e47d76a286da5369d79f2e002c87 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 14 Nov 2016 10:49:40 +1100
Subject: [PATCH] plink-ng: init at 1.90b3
---
.../science/biology/plink-ng/default.nix | 34 +++++++++++++++++++
pkgs/top-level/all-packages.nix | 2 ++
2 files changed, 36 insertions(+)
create mode 100644 pkgs/applications/science/biology/plink-ng/default.nix
diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix
new file mode 100644
index 00000000000..eb4d2714a12
--- /dev/null
+++ b/pkgs/applications/science/biology/plink-ng/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, zlib, openblas, darwin}:
+
+stdenv.mkDerivation rec {
+ name = "plink-ng-${version}";
+ version = "1.90b3";
+
+ src = fetchFromGitHub {
+ owner = "chrchang";
+ repo = "plink-ng";
+ rev = "v${version}";
+ sha256 = "1zhffjbwpd50dxywccbnv1rxy9njwz73l4awc5j7i28rgj3davcq";
+ };
+
+ buildInputs = [ zlib ] ++ (if stdenv.isDarwin then [ darwin.apple_sdk.frameworks.Accelerate ] else [ openblas ]) ;
+
+ buildPhase = ''
+ sed -i 's|zlib-1.2.8/zlib.h|zlib.h|g' *.c *.h
+ ${if stdenv.cc.isClang then "sed -i 's|g++|clang++|g' Makefile.std" else ""}
+ make ZLIB=-lz ${if stdenv.isDarwin then "" else "BLASFLAGS=-lopenblas"} -f Makefile.std
+ '';
+
+ installPhase = ''
+ mkdir -p $out/bin
+ cp plink $out/bin
+ '';
+
+ meta = {
+ description = "A comprehensive update to the PLINK association analysis toolset";
+ homepage = "https://www.cog-genomics.org/plink2";
+ license = stdenv.lib.licenses.gpl3;
+ platforms = stdenv.lib.platforms.all;
+ };
+}
+
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b3a881fc9ad..4c2690d1c65 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16350,6 +16350,8 @@ in
paml = callPackage ../applications/science/biology/paml { };
plink = callPackage ../applications/science/biology/plink/default.nix { };
+
+ plink-ng = callPackage ../applications/science/biology/plink-ng/default.nix { };
samtools = callPackage ../applications/science/biology/samtools/default.nix { };