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comparison Makefile @ 13:efb1f7698981 draft

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author malbuquerque
date Tue, 20 Jan 2015 17:12:06 -0500
parents 226f241f0c92
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12:185a2045415d 13:efb1f7698981
1 DEBUG ?= 0
2 PARALLEL ?= 0
3
4 # External Libraries
5 BOOST_ROOT ?= /g/solexa/bin/software/boost_1_53_0/
6 BAMTOOLS_ROOT ?= /g/solexa/bin/software/bamtools-2.3.0/
7 SEQTK_ROOT ?= /g/solexa/bin/software/kseq/
8
9 # Flags
10 CXX=g++
11 CXXFLAGS += -isystem ${BOOST_ROOT}/include -isystem ${BAMTOOLS_ROOT}/include -isystem ${SEQTK_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
12 LDFLAGS += -L${BOOST_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -L${BAMTOOLS_ROOT}/lib -lbamtools -lz -Wl,-rpath,${BAMTOOLS_ROOT}/lib,-rpath,${BOOST_ROOT}/lib
13
14 # Additional flags for release/debug
15 ifeq (${PARALLEL}, 1)
16 CXXFLAGS += -fopenmp -DOPENMP
17 else
18 CXXFLAGS += -DNOPENMP
19 endif
20
21 # Additional flags for release/debug
22 ifeq (${DEBUG}, 1)
23 CXXFLAGS += -g -O0 -fno-inline -DDEBUG
24 else ifeq (${DEBUG}, 2)
25 CXXFLAGS += -g -O0 -fno-inline -DPROFILE
26 LDFLAGS += -lprofiler -ltcmalloc
27 else
28 CXXFLAGS += -O9 -DNDEBUG
29 #LDFLAGS += --static
30 endif
31
32 # External sources
33 HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h)
34 BAMTOOLSSOURCES = $(wildcard src/bamtools/src/api/*.h) $(wildcard src/bamtools/src/api/*.cpp)
35 DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
36
37 # Targets
38 TARGETS = src/delly src/extract src/cov src/iover src/stats
39
40 all: $(TARGETS)
41
42 src/delly: $(DELLYSOURCES)
43 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
44
45 src/extract: $(DELLYSOURCES)
46 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
47
48 src/cov: $(DELLYSOURCES)
49 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
50
51 src/iover: $(DELLYSOURCES)
52 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
53
54 src/stats: $(DELLYSOURCES)
55 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
56
57 clean:
58 rm -f $(TARGETS) $(TARGETS:=.o)