--- Makefile.orig	2015-06-23 16:32:51 UTC
+++ Makefile
@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
 SEQAN_DIR = SeqAn-1.1
 SEQAN_INC = -I $(SEQAN_DIR)
 INC = $(SEQAN_INC) -I third_party
-CPP = g++
-CXX = $(CPP)
-CC = gcc
+
+# Use ?= to allow environment CPP, CC, CXX to take precedence.  This avoids
+# the need to modify the Makefile on different platforms.  Package managers
+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
+CPP ?= g++
+CXX ?= $(CPP)
+CC ?= gcc
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 1
@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
 PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
 
 ifeq (1,$(WITH_TBB))
-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
+	LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
 	EXTRA_FLAGS += -DWITH_TBB
 else
-	LIBS = $(PTHREAD_LIB)
+	LIBS = ${LDFLAGS} $(PTHREAD_LIB)
 endif
 
 SEARCH_LIBS = 
@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
 VERSION = $(shell cat VERSION)
 
 BITS=32
-ifeq (x86_64,$(shell uname -m))
+ifeq (amd64,$(shell uname -m))
 	BITS=64
 endif
 # msys will always be 32 bit so look at the cpu arch instead.
@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
     $(error bowtie2 compilation requires a 64-bit platform )
 endif
 
-DEBUG_FLAGS = -O0 -g3 -m64
-RELEASE_FLAGS = -O3 -m64
+DEBUG_FLAGS = -O0 -g3
+RELEASE_FLAGS = -O
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE