diff --git a/pkgs/applications/science/biology/bedops/default.nix b/pkgs/applications/science/biology/bedops/default.nix
index bde774c622bd..d455e98264cc 100644
--- a/pkgs/applications/science/biology/bedops/default.nix
+++ b/pkgs/applications/science/biology/bedops/default.nix
@@ -18,7 +18,20 @@ stdenv.mkDerivation rec {
     # We use nixpkgs versions of these libraries
     rm -r third-party
     sed -i '/^LIBS/d' system.mk/*
-    sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile
+    sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile*
+
+    # `make support` installs above libraries
+    substituteInPlace system.mk/* \
+      --replace ": support" ":"
+
+    # Variable name is different in this makefile
+    substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
+      --replace "DIST_DIR" "BINDIR"
+
+    # `mkdir -p $BINDIR` is missing
+    substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
+      --replace 'mkdir -p ''${OBJ_DIR}' 'mkdir -p ''${OBJ_DIR} ''${BINDIR}'
+
     substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' ""
 
     # Function name is different in nixpkgs provided libraries
@@ -27,7 +40,7 @@ stdenv.mkDerivation rec {
     done
 
     # Don't force static
-    for f in */*/*/*/Makefile ; do
+    for f in */*/*/*/Makefile* ; do
       substituteInPlace $f --replace '-static' ""
     done
   '';
@@ -46,6 +59,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Only;
     maintainers = with maintainers; [ jbedo ];
     platforms = platforms.x86_64;
-    broken = stdenv.isDarwin;
   };
 }