blob: c668d5c6154eda73fa1f6036ee84f4142b4abfa3 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
|
Fix build system, in order to honour user variables
--- a/makefile
+++ b/makefile
@@ -1,7 +1,4 @@
-
-CC = g++ -Wall -ggdb
-CC = g++ -pg
-CC = g++
+CXX ?= g++
# without OpenMP
@@ -9,35 +6,19 @@
# in command line:
# make openmp=yes
ifeq ($(openmp),no)
- CCFLAGS = -DNO_OPENMP
-else
- CCFLAGS = -fopenmp
-endif
-
-# support debugging
-# in command line:
-# make debug=yes
-# make openmp=yes debug=yes
-ifeq ($(debug),yes)
-CCFLAGS += -ggdb
+ my_CPPFLAGS = -DNO_OPENMP
else
-CCFLAGS += -O2
+ my_CXXFLAGS = -fopenmp
endif
ifdef MAX_SEQ
-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ)
endif
-#LDFLAGS = -static -o
-LDFLAGS += -o
-
PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
-# Propagate hardening flags
-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
-
.c++.o:
- $(CC) $(CCFLAGS) -c $<
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $<
all: $(PROGS)
@@ -47,52 +28,52 @@
# programs
cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
# objects
cdhit-common.o: cdhit-common.c++ cdhit-common.h
- $(CC) $(CCFLAGS) cdhit-common.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c
cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
- $(CC) $(CCFLAGS) cdhit-utility.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c
cdhit.o: cdhit.c++ cdhit-utility.h
- $(CC) $(CCFLAGS) cdhit.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c
cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
- $(CC) $(CCFLAGS) cdhit-2d.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c
cdhit-est.o: cdhit-est.c++ cdhit-utility.h
- $(CC) $(CCFLAGS) cdhit-est.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c
cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c
cdhit-div.o: cdhit-div.c++ cdhit-common.h
- $(CC) $(CCFLAGS) cdhit-div.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c
cdhit-454.o: cdhit-454.c++ cdhit-common.h
- $(CC) $(CCFLAGS) cdhit-454.c++ -c
+ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c
PREFIX ?= /usr/local/bin
install:
for prog in $(PROGS); do \
- install -m 0755 $$prog $(PREFIX); \
+ install -m 0755 $$prog $(DESTDIR)$(PREFIX); \
done
- install -m 0755 *.pl $(PREFIX);
+ install -m 0755 *.pl $(DESTDIR)$(PREFIX);
|
GitWeb