3 files changed, 17 insertions, 9 deletions
diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 406f42e9ad7b..2cdd7fda38ef 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,17 +1,17 @@
-{stdenv, fetchFromGitHub, zlib, python}:
+{stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
 
 stdenv.mkDerivation rec {
   name = "bedtools-${version}";
-  version = "2.27.1";
+  version = "2.28.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s";
+    sha256 = "1266bcn5hgbvysfi6nr4cqxlbxcx7vn7ng8kb0v3gz37qh2zxxw9";
   };
 
-  buildInputs = [ zlib python ];
+  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";
diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index 3367fa87422b..153ebaa441f5 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -53,7 +53,7 @@ stdenv.mkDerivation rec {
   cmakeFlags =
     # It's important that caffe is passed the major and minor version only because that's what
     # boost_python expects
-    [ (if pythonSupport then "-Dpython_version=3${python.pythonVersion}" else "-DBUILD_python=OFF")
+    [ (if pythonSupport then "-Dpython_version=${python.pythonVersion}" else "-DBUILD_python=OFF")
       "-DBLAS=open"
     ] ++ (if cudaSupport then [
            "-DCUDA_ARCH_NAME=All"
@@ -73,9 +73,17 @@ stdenv.mkDerivation rec {
                 ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]
                 ;
 
-  propagatedBuildInputs = lib.optional pythonSupport python.pkgs.protobuf;
-
-  outputs = [ "bin" "out"];
+  propagatedBuildInputs = lib.optionals pythonSupport (
+    # requirements.txt
+    let pp = python.pkgs; in ([
+      pp.numpy pp.scipy pp.scikitimage pp.h5py
+      pp.matplotlib pp.ipython pp.networkx pp.nose
+      pp.pandas pp.dateutil pp.protobuf pp.gflags
+      pp.pyyaml pp.pillow pp.six
+    ] ++ lib.optional leveldbSupport pp.leveldb)
+  );
+
+  outputs = [ "bin" "out" ];
   propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
 
   patches = [
diff --git a/pkgs/applications/science/math/caffe/python.patch b/pkgs/applications/science/math/caffe/python.patch
index b1bed6c174b8..dac5071aa08c 100644
--- a/pkgs/applications/science/math/caffe/python.patch
+++ b/pkgs/applications/science/math/caffe/python.patch
@@ -64,7 +64,7 @@ index 4a5bac47..be026d43 100644
 -  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND)
 +  find_package(NumPy 1.7.1)
 +  find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@)
-+  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND BOOST_PYTHON@major@@minor@_FOUND)
++  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON@major@@minor@_FOUND)
      set(HAVE_PYTHON TRUE)
      if(BUILD_python_layer)
        list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER)