--- a/Makefile
+++ b/Makefile
@@ -4,44 +4,29 @@
 # (c) 2009 Aaron Quinlan
 # ==========================
 
-SHELL := /bin/bash -e
+SHELL := bash -e
 
 VERSION_FILE=./src/utils/version/version_git.h
 RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
 
 
 # define our object and binary directories
-ifeq ($(VERBOSE),1)
 CCPREFIX =
-else
-CCPREFIX = @
-endif
 
 OBJ_DIR	= obj
 BIN_DIR	= bin
 SRC_DIR	= src
 
-CXX     = g++
-
-ifeq ($(DEBUG),1)
-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
-else
 BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-BT_CXXFLAGS = -g -Wall -O2
-endif
+BT_CXXFLAGS = -Wall
 
 # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
-ifeq ($(USE_RAND),1)
-BT_CXXFLAGS += -DUSE_RAND
-else
 BT_CXXFLAGS += -std=c++11
-endif
 
 BT_LDFLAGS =
 BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
 
-prefix ?= /usr/local
+prefix = $(EPREFIX)/usr
 
 SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/bamToBed \
@@ -204,7 +189,7 @@
 
 # make the "obj/" and "bin/" directories, if they don't exist
 $(OBJ_DIR) $(BIN_DIR):
-	@mkdir -p $@
+	mkdir -p $@
 
 
 # Usually HTSlib's configure script has not been used (detected via config.mk
--- a/src/utils/htslib/Makefile
+++ b/src/utils/htslib/Makefile
@@ -22,20 +22,13 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
-
 # Default libraries to link if configure is not used
 htslib_default_libs = -lz -lm -lbz2 -llzma
 
-CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS   = -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
 LIBS     = $(htslib_default_libs)
 
 prefix      = /usr/local