From f7a4e4a93a2a317fb76b9e09a97ea6246e477da2 Mon Sep 17 00:00:00 2001
From: Bruno Bzeznik <Bruno.Bzeznik@imag.fr>
Date: Thu, 9 Jan 2020 18:38:54 +0100
Subject: [PATCH] bayescan: init at 2.1 (#68191)

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
---
 .../science/biology/bayescan/default.nix      | 39 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 41 insertions(+)
 create mode 100644 pkgs/applications/science/biology/bayescan/default.nix

diff --git a/pkgs/applications/science/biology/bayescan/default.nix b/pkgs/applications/science/biology/bayescan/default.nix
new file mode 100644
index 000000000000..4e216fbdbe63
--- /dev/null
+++ b/pkgs/applications/science/biology/bayescan/default.nix
@@ -0,0 +1,39 @@
+{ stdenv, fetchurl, unzip, llvmPackages }:
+
+stdenv.mkDerivation rec {
+  pname = "bayescan";
+  version = "2.1";
+
+  src = fetchurl {
+    url = "http://cmpg.unibe.ch/software/BayeScan/files/BayeScan${version}.zip";
+    sha256 = "0ismima8j8z0zj9yc267rpf7z90w57b2pbqzjnayhc3ab8mcbfy6";
+  };
+
+  nativeBuildInputs = [ unzip ];
+  buildInputs = stdenv.lib.optional stdenv.cc.isClang llvmPackages.openmp;
+
+  # Disable FORTIFY_SOURCE or the binary fails with "buffer overflow"
+  hardeningDisable = [ "fortify" ];
+
+  sourceRoot = "BayeScan${version}/source";
+
+  postPatch = ''
+    substituteInPlace Makefile --replace "-static" "" \
+                               --replace "g++" "c++"
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mkdir -p $out/share/doc/bayescan
+    cp bayescan_${version} $out/bin
+    cp -r ../*pdf ../input_examples ../"R functions" $out/share/doc/bayescan
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Detecting natural selection from population-based genetic data";
+    homepage = "http://cmpg.unibe.ch/software/BayeScan";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.bzizou ];
+    platforms = stdenv.lib.platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6f7011fc8741..5042a17c8463 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23701,6 +23701,8 @@ in
     stdenv = gcc49Stdenv;
   };
 
+  bayescan = callPackage ../applications/science/biology/bayescan { };
+
   bedtools = callPackage ../applications/science/biology/bedtools { };
 
   bcftools = callPackage ../applications/science/biology/bcftools { };