[ViewVC] Annotation of: gclib/tophat_cpp/Makefile

# Directories to search for header files
SEQAN = ./SeqAn-1.3
SEARCHDIRS := -I. -I${SEQAN} -I.. -I/opt/geo/include

SYSTYPE :=     $(shell uname)

# C compiler

MACHTYPE :=     $(shell uname -m)
ifeq ($(MACHTYPE), i686)
    MARCH = -march=i686
else
    MARCH = 
endif    

CC      := g++
BASEFLAGS  = -Wall -pthread ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \
-fno-strict-aliasing -D_REENTRANT


ifeq ($(findstring nodebug,$(MAKECMDGOALS)),)
  CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS)
  LDFLAGS = -g -L/opt/geo/lib
else
  CFLAGS = -O2 -DNDEBUG $(BASEFLAGS)
  LDFLAGS = -L/opt/geo/lib
endif

%.o : %.c
        ${CC} ${CFLAGS} -c $< -o $@

%.o : %.cc
        ${CC} ${CFLAGS} -c $< -o $@

%.o : %.C
        ${CC} ${CFLAGS} -c $< -o $@

%.o : %.cpp
        ${CC} ${CFLAGS} -c $< -o $@

%.o : %.cxx
        ${CC} ${CFLAGS} -c $< -o $@

# C/C++ linker

LINKER    := g++
LIBS = -lz -lbam 
BLIBS = ${LIBS} -lpthread -lboost_thread

COM_OBJS = common.o reads.o tokenize.o utils.o
PREP_OBJS = ${COM_OBJS} qual.o
GFF_OBJS  = GBase.o GStr.o codons.o gdna.o GFaSeqGet.o gff.o
SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o insertions.o coverage.o \
fragments.o align_status.o deletions.o fusions.o

ALL_EXE = fix_map_ordering map2gtf gtf_to_fasta bam_merge bam2fastx \
prep_reads extract_reads juncs_db long_spanning_reads gtf_juncs segment_juncs \
tophat_reports

.PHONY : all
#all: fix_map_ordering
all: prep_reads
#.PHONY : nodebug
nodebug : all
#all: prep_reads
#debug: prep_reads

all_exe: $(ALL_EXE)
#all: $(ALL_EXE)
#debug: $(ALL_EXE)
#all: segment_juncs
#debug: segment_juncs
#all: bam_dump
#all: sam2bam
#debug: sam2bam
#all: prep_reads
#debug: prep_reads
sam2bam: ./sam2bam.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
bam_dump: ./bam_dump.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
#all: prep_reads
#debug: prep_reads
all_bin: ${ALL_EXE}
bwt2sam: ${COM_OBJS} bwt_map.o bwt2sam.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
bam2bed: ./bam2bed.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
bam2fastx: ./bam2fastx.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
bam_merge: ./common.o ./GBase.o ./bam_merge.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
bwt_map.o: bwt_map.h
fix_map_ordering: ${COM_OBJS} bwt_map.o fix_map_ordering.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
long_spanning_reads: ${SEG_OBJS} fusions.o long_spanning_reads.o 
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
prep_reads: ${PREP_OBJS} prep_reads.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
extract_reads: ${COM_OBJS} extract_reads.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
gtf_to_fasta: ${COM_OBJS} bwt_map.o ${GFF_OBJS} FastaTools.o GTFToFasta.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} map2gtf.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} gtf_juncs.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
segment_juncs: ${SEG_OBJS} segment_juncs.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
juncs_db: ${SEG_OBJS} juncs_db.o
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
tophat_reports: ${SEG_OBJS} inserts.o tophat_reports.o 
        ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
tophat_reports.o prep_reads.o fix_map_ordering.o map2gtf.o bam_merge.o bam2fastx.o bwt_map.o common.o: common.h
bwt_map.o: common.h bwt_map.h

# target for removing all object files

.PHONY : clean
clean::
        ${RM} *.o sam2bam core core.* ${ALL_EXE}
Revision:	207
Committed:	Mon Mar 12 21:39:30 2012 UTC (12 years, 5 months ago) by gpertea
File size:	3652 byte(s)
Log Message:	wip
Line	User	Rev	File contents
1	gpertea	29	# Directories to search for header files
2	gpertea	200	SEQAN = ./SeqAn-1.3
3	gpertea	135	SEARCHDIRS := -I. -I${SEQAN} -I.. -I/opt/geo/include
4	gpertea	29
5			SYSTYPE := $(shell uname)
6
7			# C compiler
8
9			MACHTYPE := $(shell uname -m)
10			ifeq ($(MACHTYPE), i686)
11			MARCH = -march=i686
12			else
13			MARCH =
14			endif
15
16			CC := g++
17	gpertea	154	BASEFLAGS = -Wall -pthread ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \
18	gpertea	29	-fno-strict-aliasing -D_REENTRANT
19
20
21	gpertea	163	ifeq ($(findstring nodebug,$(MAKECMDGOALS)),)
22			CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS)
23			LDFLAGS = -g -L/opt/geo/lib
24			else
25	gpertea	29	CFLAGS = -O2 -DNDEBUG $(BASEFLAGS)
26			LDFLAGS = -L/opt/geo/lib
27			endif
28
29			%.o : %.c
30			${CC} ${CFLAGS} -c $< -o $@
31
32			%.o : %.cc
33			${CC} ${CFLAGS} -c $< -o $@
34
35			%.o : %.C
36			${CC} ${CFLAGS} -c $< -o $@
37
38			%.o : %.cpp
39			${CC} ${CFLAGS} -c $< -o $@
40
41			%.o : %.cxx
42			${CC} ${CFLAGS} -c $< -o $@
43
44			# C/C++ linker
45
46			LINKER := g++
47	gpertea	167	LIBS = -lz -lbam
48			BLIBS = ${LIBS} -lpthread -lboost_thread
49	gpertea	29
50	gpertea	154	COM_OBJS = common.o reads.o tokenize.o utils.o
51	gpertea	29	PREP_OBJS = ${COM_OBJS} qual.o
52			GFF_OBJS = GBase.o GStr.o codons.o gdna.o GFaSeqGet.o gff.o
53	gpertea	200	SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o insertions.o coverage.o \
54			fragments.o align_status.o deletions.o fusions.o
55	gpertea	29
56	gpertea	135	ALL_EXE = fix_map_ordering map2gtf gtf_to_fasta bam_merge bam2fastx \
57	gpertea	167	prep_reads extract_reads juncs_db long_spanning_reads gtf_juncs segment_juncs \
58	gpertea	135	tophat_reports
59	gpertea	29
60			.PHONY : all
61	gpertea	167	#all: fix_map_ordering
62	gpertea	207	all: prep_reads
63	gpertea	163	#.PHONY : nodebug
64			nodebug : all
65	gpertea	135	#all: prep_reads
66			#debug: prep_reads
67
68	gpertea	157	all_exe: $(ALL_EXE)
69	gpertea	135	#all: $(ALL_EXE)
70			#debug: $(ALL_EXE)
71			#all: segment_juncs
72			#debug: segment_juncs
73	gpertea	29	#all: bam_dump
74			#all: sam2bam
75			#debug: sam2bam
76			#all: prep_reads
77			#debug: prep_reads
78			sam2bam: ./sam2bam.o
79			${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
80			bam_dump: ./bam_dump.o
81			${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
82			#all: prep_reads
83			#debug: prep_reads
84			all_bin: ${ALL_EXE}
85			bwt2sam: ${COM_OBJS} bwt_map.o bwt2sam.o
86			${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
87			bam2bed: ./bam2bed.o
88			${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
89			bam2fastx: ./bam2fastx.o
90			${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
91	gpertea	157	bam_merge: ./common.o ./GBase.o ./bam_merge.o
92	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
93			bwt_map.o: bwt_map.h
94	gpertea	200	fix_map_ordering: ${COM_OBJS} bwt_map.o fix_map_ordering.o
95	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
96	gpertea	154	long_spanning_reads: ${SEG_OBJS} fusions.o long_spanning_reads.o
97	gpertea	167	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
98	gpertea	200	prep_reads: ${PREP_OBJS} prep_reads.o
99	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
100	gpertea	200	extract_reads: ${COM_OBJS} extract_reads.o
101	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
102	gpertea	200	gtf_to_fasta: ${COM_OBJS} bwt_map.o ${GFF_OBJS} FastaTools.o GTFToFasta.o
103	gpertea	135	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
104	gpertea	200	map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} map2gtf.o
105	gpertea	135	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
106	gpertea	200	gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} gtf_juncs.o
107	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
108	gpertea	200	segment_juncs: ${SEG_OBJS} segment_juncs.o
109	gpertea	167	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
110	gpertea	200	juncs_db: ${SEG_OBJS} juncs_db.o
111	gpertea	29	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
112	gpertea	200	tophat_reports: ${SEG_OBJS} inserts.o tophat_reports.o
113	gpertea	167	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
114	gpertea	200	tophat_reports.o prep_reads.o fix_map_ordering.o map2gtf.o bam_merge.o bam2fastx.o bwt_map.o common.o: common.h
115			bwt_map.o: common.h bwt_map.h
116	gpertea	29
117			# target for removing all object files
118
119			.PHONY : clean
120	gpertea	135	clean::
121			${RM} .o sam2bam core core. ${ALL_EXE}