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comparison ezBAMQC/Makefile @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 # Makefile for ezBAMQC, utilities for the Sequence Alignment/Map format.
2 #
3 # Version 0.6.5
4 #
5 # Copyright (C) 2015 Bioinformatics Shared Resource, CSHL.
6 # Portions copyright (C) 2015 Cold Spring Harbor Laboratory.
7 #
8 # Permission is hereby granted, free of charge, to any person obtaining a copy
9 # of this software and associated documentation files (the "Software"), to deal
10 # in the Software without restriction, including without limitation the rights
11 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12 # copies of the Software, and to permit persons to whom the Software is
13 # furnished to do so, subject to the following conditions:
14 #
15 # The above copyright notice and this permission notice shall be included in
16 # all copies or substantial portions of the Software.
17 #
18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
21 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
23 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
24 # DEALINGS IN THE SOFTWARE.
25
26 CC = g++
27 CPPFLAGS = $(DFLAGS) $(INCLUDES)
28 CFLAGS = -g -fpermissive -Wall -O9 -O3 -std=c++11 -fPIC
29 LDFLAGS = -O9 -fpermissive
30 LDLIBS =
31 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
32 LOBJS= src/ezBAMQC/GeneFeatures.o src/ezBAMQC/rRNA.o src/ezBAMQC/IntervalTree.o src/ezBAMQC/InnerDist_prof.o \
33 src/ezBAMQC/Results.o src/ezBAMQC/Mappability.o src/ezBAMQC/Coverage_prof.o src/ezBAMQC/parseBAM.o
34
35 INCLUDES= -I$(HTSDIR)
36 LIBCURSES= -lcurses # -lXCurses
37
38 prefix = /usr/local
39 exec_prefix = $(prefix)
40 bindir = $(exec_prefix)/bin
41 mandir = $(prefix)/share/man
42 man1dir = $(mandir)/man1
43
44 MKDIR_P = mkdir -p
45 #INSTALL = install -p
46 #INSTALL_PROGRAM = $(INSTALL)
47 #INSTALL_DATA = $(INSTALL) -m 644
48 #INSTALL_DIR = $(MKDIR_P) -m 755
49
50
51 PROGRAMS = libBAMqc.so
52
53
54 all: $(PROGRAMS)
55
56
57 # Adjust $(HTSDIR) to point to your top-level htslib directory
58 HTSDIR = ./src/htslib
59 include $(HTSDIR)/htslib.mk
60 HTSLIB = $(HTSDIR)/libhts.a
61 BGZIP = $(HTSDIR)/bgzip
62
63
64 PACKAGE_VERSION = 0.5
65
66
67 .SUFFIXES: .cpp .o
68
69 .cpp.o:
70 $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
71
72
73 #lib:libbam.a
74
75 #libbam.a:$(LOBJS)
76 # $(AR) -csru $@ $(LOBJS)
77
78 #libBAMqc.so: $(LOBJS) $(HTSLIB)
79 # $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
80
81 libBAMqc.so: $(LOBJS) $(HTSLIB)
82 # $(CC) -shared -Wl,-soname, libBAMqc.so.$(PACKAGE_VERSION) -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
83 $(CC) -shared -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
84 # ln -sf $@ libBAMqc.so.$(PACKAGE_VERSION)
85
86 Constants_h = src/ezBAMQC/Constants.h
87 IntervalTree_h = src/ezBAMQC/IntervalTree.h $(Constants_h)
88 GeneFeatures_h = src/ezBAMQC/GeneFeatures.h $(Constants_h)
89 rRNA_h = src/ezBAMQC/rRNA.h $(IntervalTree_h) $(GeneFeatures_h)
90 Results_h = src/ezBAMQC/Resualts.h
91 Mappability_h = src/ezBAMQC/Mappability.h $(Constants_h)
92 InnerDist_prof_h = src/ezBAMQC/InnerDist_prof.h $(GeneFeatures_h)
93 Coverage_prof_h = src/ezBAMQC/Coverage_prof.h $(GeneFeatures_h)
94 parseBAM_h = src/ezBAMQC/parseBAM.h
95
96
97 IntervalTree.o: src/ezBAMQC/IntervalTree.cpp $(IntervalTree_h)
98 GeneFeatures.o: src/ezBAMQC/GeneFeatures.cpp $(GeneFeatures_h)
99 rRNA.o: src/ezBAMQC/rRNA.cpp $(rRNA_h)
100 Results.o: src/ezBAMQC/Results.cpp $(Results_h)
101 Mappability.o: src/ezBAMQC/Mappability.cpp $(Mappability_h) $(htslib_sam_h)
102 InnerDist_prof.o: src/ezBAMQC/InnerDist_prof.cpp $(InnerDist_prof_h) $(htslib_sam_h)
103 Coverage_prof.o: src/ezBAMQC/Coverage_prof.cpp $(Coverage_prof_h)
104 parseBAM.o: src/ezBAMQC/parseBAM.cpp $(parseBAM_h) $(htslib_sam_h) $(GeneFeatures_h) $(rRNA_h) $(Mappability_h) $(Coverage_prof_h) $(InnerDist_prof_h)
105
106
107 #install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
108 # $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
109 # $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
110 # $(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)
111
112
113 mostlyclean:
114 -rm -f src/*.o
115
116 clean: mostlyclean
117 -rm -f $(PROGRAMS)
118
119 distclean: clean
120 -rm -f TAGS
121
122 clean-all: clean
123
124
125 tags:
126 ctags -f TAGS *.[ch] misc/*.[ch]
127
128
129 force:
130
131
132 .PHONY: all clean clean-all distclean force
133 .PHONY: mostlyclean tags