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
123
124
125
126
127
128
129
130
131
132
|
########################################################################
# Generic command-line makefile for NCBI applications
#
# This assumes the following variables are set in a file called "ncbi.mk"
# which is included by this one. In this case it resides in a directory
# set by the environment variable "NCBI"
#
# NCBI_CC = default compiler to use
# NCBI_CFLAGS1 = default compiler switches (not optimization)
# NCBI_LDFLAGS1 = default compiler switches when linking (not optimization)
# NCBI_OPTFLAG = default optimization (-O)
# NCBI_INCDIR = default toolkit include paths
# NCBI_LIBDIR = default toolkit library paths
# NCBI_ALTLIB = debugging toolkit library paths
# NCBI_VIBFLAG = additional include paths/defines for Vibrant apps
# NCBI_VIBLIBS = additional libraries needed to link Vibrant apps
# NCBI_OTHERLIBS = additional libraries needed to link the system
#
# This enables platform independent makefiles for ncbi toolkit apps. You
# can change any default behavior by setting the variable on the command
# line.
#
# Use gcc complier. "make NCBI_CC=gcc" or "make CC=gcc"
# Change optimization to debug
# "make NCBI_OPTFLAG="-g" NCBI_LIBPATH=$NCBI_ALTLIB"
# or
# "make OPTFLAG="-g" LIBPATH=$NCBI_ALTLIB"
#
# You can also change the behavior permanently in the makefile by changing
# the assignment of the internal variable to the one from the include
# file:
#
# Use gcc compiler.
# Change CC=$(NCBI_CC)
# To CC=gcc
# in the makefile itself
#
# Make debugging version
# OPTFLAG=-g
# LIBPATH=$(NCBI_ALTLIB)
#
# You need to specify the EXE and SRC symbols
#
#######################################################################
#
# default flags for compiling and loading
#
#######################################################################
include $(NCBI)/ncbi.mk
CC = $(NCBI_CC)
#CC = lint
#CC = purify cc -xildoff
CFLAGS1 = $(NCBI_CFLAGS1)
LDFLAGS1 = $(NCBI_LDFLAGS1)
OPTFLAG = -g -D DEBUG_DDV
OTHERLIBS = $(NCBI_OTHERLIBS)
VIBLIBS= $(NCBI_VIBLIBS)
VIBFLAG= $(NCBI_VIBFLAG)
INCPATH = $(NCBI_INCDIR)
LIBPATH = $(NCBI_ALTLIB)
# DEF = -DINTERNAL_NCBI_SEQUIN -DSALSA_DEBUG
SRC = algorend.o cn3dentr.o cn3dmain.o cn3dmatn.o cn3dmesh.o cn3dmodl.o \
cn3dmsel.o cn3dmsg.o cn3dopen.o cn3dsave.o cn3dshim.o \
cn3dwin.o cn3dxprt.o seqcons.o cn3dstyl.o
EXE = Cn3D
CFLAGS = $(CFLAGS1) $(OPTFLAG) -I. -I$(INCPATH) $(VIBFLAG) $(DEF)
LDFLAGS = -I. -I$(INCPATH) $(OPTFLAG) -L../lib -L$(LIBPATH) $(VIBFLAG) $(DEF)
# all NCBI libraries aliased for easy access here
LIB1 = -lncbi
LIB2 = -lncbiobj
LIB3 = -lncbicdr
LIB4 = -lvibrant
LIB5 = -lncbiacc
LIB6 = -lnetcli
LIB7 = -lnetentr
LIB8 = -lncbiNacc
LIB9 = -lncbiCacc
# LIB10 is reserved for NCSA socket library
#LIB10 =
LIB11 = -lncbimla
LIB12 = -lncbitax1
LIB13 = -lncbiid0
LIB18 = -lncbibls2
LIB19 = -lncbispel
LIB20 = -lncbidesk
LIB21 = -lncbibls2
LIB22 = -lncbimmdb
LIB23 = -lncbitool
LIB29 = -lncbitxc1
LIB31 = -lvibnet
LIB33 = -lsmartnet
LIB36 = -lncbitree
LIB41 = -lncbiid1
## To clean out the directory without removing make
##
## Implicit actions
##
## if need a .o, compile the .c
##
.KEEP_STATE:
.c.o :
$(CC) $(CFLAGS) $<
#####################################################################
##
## Here is where you set up your own things to make
##
#####################################################################
## Default thing to make will be "all"
##
all : $(EXE)
## make individual applications and components
##
$(EXE) : $(SRC)
$(CC) -o $(EXE) $(LDFLAGS) $(SRC) $(LIB31) $(LIB20) $(LIB41) -lnetblast $(LIB22) \
$(LIB8) $(LIB7) $(LIB6) $(LIB3) $(LIB4) $(LIB23) $(LIB2) $(LIB1) \
$(NCBI_VIBLIBS) $(LIB36) $(NCBI_OTHERLIBS)
|
