From 592d288aa2969cdaa23ad1f51a33dfc89493dda8 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 10 Dec 2019 13:24:27 +1100
Subject: [PATCH 1/2] bedtools: 2.29.0 -> 2.29.1

---
 pkgs/applications/science/biology/bedtools/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 4e4c093ad7f..695cf7c48c3 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
-  version = "2.29.0";
+  version = "2.29.1";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "0d6i985qqxp92ddq4n6558m70qi5rqhl724wrfys0hm0p6a9h56x";
+    sha256 = "1vbpjvzl4ppzkan9qgm84bkn9kl3h3m5xz92y18wn1sksxcdq50x";
   };
 
   buildInputs = [ zlib python bzip2 lzma ];

From 50fbca4bfceb6df7e45043707083e1671bec6dd9 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 11 Dec 2019 09:27:57 +1100
Subject: [PATCH 2/2] bedtools: fix clang builds

---
 pkgs/applications/science/biology/bedtools/default.nix | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 695cf7c48c3..0bb5ee866e5 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -12,9 +12,10 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [ zlib python bzip2 lzma ];
-  cc = if stdenv.cc.isClang then "clang++" else "g++";
-  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
-  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
+  cxx = if stdenv.cc.isClang then "clang++" else "g++";
+  cc = if stdenv.cc.isClang then "clang" else "gcc";
+  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
+  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install";
 
   meta = with stdenv.lib; {
     description = "A powerful toolset for genome arithmetic.";