--- Makefile.orig	2016-12-30 15:40:06 UTC
+++ Makefile
@@ -21,8 +21,8 @@
 # Makefile for bowtie, bowtie2-build, bowtie2-inspect
 #
 
-prefix = /usr/local
-bindir = $(prefix)/bin
+PREFIX ?= /usr/local
+bindir = $(PREFIX)/bin
 
 INC =
 GCC_PREFIX = $(shell dirname `which gcc`)
@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
     INC += -I third_party
 endif
 
+INC += -I ${LOCALBASE}/include
+
 MM_DEF =
 
 ifeq (1,$(BOWTIE_MM))
@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
 endif
 
 PTHREAD_PKG =
-PTHREAD_LIB =
+PTHREAD_LIB = 
 
 #if we're not using TBB, then we can't use queuing locks
 ifeq (1,$(NO_TBB))
@@ -94,7 +96,7 @@ endif
 
 #default is to use Intel TBB
 ifneq (1,$(NO_TBB))
-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
+	LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
 	override EXTRA_FLAGS += -DWITH_TBB
 else
 	LIBS = $(PTHREAD_LIB)
@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
 
 DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS  = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
+RELEASE_FLAGS  = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops
 RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
