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Enable compilation on FreeBSD + clang. #19

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Enable compilation on FreeBSD + clang. #19

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18 changes: 15 additions & 3 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ 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
CPP ?= g++
CXX ?= $(CPP)
CC ?= gcc
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I think this part is useful. Not only when building by clang but also building by gcc-N compiler.

HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 1
Expand Down Expand Up @@ -61,6 +61,12 @@ ifneq (,$(findstring Linux,$(shell uname)))
EXTRA_FLAGS += -Wl,--hash-style=both
endif

FREEBSD = 0
ifneq (,$(findstring FreeBSD,$(shell uname)))
FREEBSD = 1
EXTRA_FLAGS += -Wl,--hash-style=both
endif

MM_DEF =
ifeq (1,$(BOWTIE_MM))
MM_DEF = -DBOWTIE_MM
Expand Down Expand Up @@ -139,6 +145,12 @@ ifeq (1,$(LINUX))
endif
endif

ifeq (1,$(FREEBSD))
ifeq (amd64, $(shell uname -p))
BITS=64
endif
endif

ifeq (32,$(BITS))
$(error bowtie2 compilation requires a 64-bit platform )
endif
Expand Down