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
|
#-- Imported variables from top level makefile
# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
ifndef BIN_DIR
BIN_DIR := $(CURDIR)
endif
ifndef INSTALL_BIN_DIR
FINAL_BIN_DIR := $(BIN_DIR)
endif
ifndef AUX_BIN_DIR
AUX_BIN_DIR := $(CURDIR)
endif
ifndef INSTALL_AUX_BIN_DIR
FINAL_AUX_BIN_DIR := $(BIN_DIR)
endif
ifndef SCRIPT_DIR
SCRIPT_DIR := $(CURDIR)
endif
SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
VPATH := $(BIN_DIR)
ALL := exact-tandems mapview mummerplot nucmer promer \
run-mummer1 run-mummer3 nucmer2xfig dnadiff
#-- PHONY rules --#
.PHONY: all clean
all: $(ALL)
clean:
rm -f *~
cd $(BIN_DIR); rm -f $(ALL)
#-- not so PHONY rules --#
exact-tandems: ../debian/sh-replacement-scripts/exact-tandems
cp -a $^ $(BIN_DIR)
chmod 755 $(BIN_DIR)/exact-tandems
mapview: mapview.pl
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
mapview.pl > $(BIN_DIR)/mapview
chmod 755 $(BIN_DIR)/mapview
mummerplot: mummerplot.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
-e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
mummerplot.pl > $(BIN_DIR)/mummerplot
chmod 755 $(BIN_DIR)/mummerplot
dnadiff: dnadiff.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
-e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
dnadiff.pl > $(BIN_DIR)/dnadiff
chmod 755 $(BIN_DIR)/dnadiff
nucmer: nucmer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
-e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
-e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
nucmer.pl > $(BIN_DIR)/nucmer
chmod 755 $(BIN_DIR)/nucmer
promer: promer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
-e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
-e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
promer.pl > $(BIN_DIR)/promer
chmod 755 $(BIN_DIR)/promer
run-mummer1: ../debian/sh-replacement-scripts/run-mummer1
cp -a $^ $(BIN_DIR)
chmod 755 $(BIN_DIR)/run-mummer1
run-mummer3: ../debian/sh-replacement-scripts/run-mummer3
cp -a $^ $(BIN_DIR)
chmod 755 $(BIN_DIR)/run-mummer3
nucmer2xfig: nucmer2xfig.pl
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
chmod 755 $(BIN_DIR)/nucmer2xfig
|
