From 59ca5d213f99d10f9cc187763876b5c4008bac7d Mon Sep 17 00:00:00 2001
From: Jason Daniel Augustine Gilliland <jdagilliland@gmail.com>
Date: Sat, 17 Dec 2016 00:36:53 -0500
Subject: [PATCH] freebayes: init at 1.1.0

Signed-off-by: zimbatm <zimbatm@zimbatm.com>
---
 lib/maintainers.nix                           |  1 +
 .../science/biology/freebayes/builder.sh      | 11 ++++++++
 .../science/biology/freebayes/default.nix     | 27 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 4 files changed, 41 insertions(+)
 create mode 100644 pkgs/applications/science/biology/freebayes/builder.sh
 create mode 100644 pkgs/applications/science/biology/freebayes/default.nix

diff --git a/lib/maintainers.nix b/lib/maintainers.nix
index f88cd1212fb0..7ed8ae953bc0 100644
--- a/lib/maintainers.nix
+++ b/lib/maintainers.nix
@@ -206,6 +206,7 @@
   jb55 = "William Casarin <bill@casarin.me>";
   jbedo = "Justin Bedő <cu@cua0.org>";
   jcumming = "Jack Cummings <jack@mudshark.org>";
+  jdagilliland = "Jason Gilliland <jdagilliland@gmail.com>";
   jefdaj = "Jeffrey David Johnson <jefdaj@gmail.com>";
   jerith666 = "Matt McHenry <github@matt.mchenryfamily.org>";
   jfb = "James Felix Black <james@yamtime.com>";
diff --git a/pkgs/applications/science/biology/freebayes/builder.sh b/pkgs/applications/science/biology/freebayes/builder.sh
new file mode 100644
index 000000000000..a9f56e77d7e3
--- /dev/null
+++ b/pkgs/applications/science/biology/freebayes/builder.sh
@@ -0,0 +1,11 @@
+source $stdenv/setup
+
+unpackPhase
+
+cd freebayes-*
+
+make
+
+mkdir -p $out/bin
+cp bin/freebayes bin/bamleftalign $out/bin
+cp scripts/* $out/bin
diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix
new file mode 100644
index 000000000000..ef0da619b25a
--- /dev/null
+++ b/pkgs/applications/science/biology/freebayes/default.nix
@@ -0,0 +1,27 @@
+{ stdenv, fetchFromGitHub, cmake, gcc, zlib}:
+
+stdenv.mkDerivation rec {
+  name    = "freebayes-${version}";
+  version = "1.1.0";
+
+  src = fetchFromGitHub {
+    name = "freebayes-${version}-src";
+    owner  = "ekg";
+    repo   = "freebayes";
+    rev    = "refs/tags/v${version}";
+    sha256 = "0xb8aicb36w9mfs1gq1x7mcp3p82kl7i61d162hfncqzg2npg8rr";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ cmake gcc zlib ];
+
+  builder = ./builder.sh;
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based polymorphism discovery and genotyping";
+    license     = licenses.mit;
+    homepage    = https://github.com/ekg/freebayes;
+    maintainers = with maintainers; [ jdagilliland ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 4261200ad6c7..82c131b901a0 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -12994,6 +12994,8 @@ in
 
   fossil = callPackage ../applications/version-management/fossil { };
 
+  freebayes = callPackage ../applications/science/biology/freebayes { };
+
   freewheeling = callPackage ../applications/audio/freewheeling { };
 
   fribid = callPackage ../applications/networking/browsers/mozilla-plugins/fribid { };