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
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# INSTALLING GFF2APLOT FILES
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# The following Makefile was developed
# on a Red Hat Linux box running on GNU Make version 3.79.1
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
# Thomas WIEHE
# Roderic GUIGO SERRA
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# $Id: dist_Makefile,v 1.1 2003/03/17 17:58:46 jabril Exp $
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# INSTALLDIR is the only variable that should be modified
# (unless you were not using GNUmake, of course, because in such
# case you must fix all the GNUmake specific commands... ;^D).
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
### PATHS
BBIN = /bin
UBIN = /usr/bin
LBIN = /usr/local/bin
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# REMEMBER: INSTALLDIR is the only variable that should be modified
INSTALLDIR = $(LBIN)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
### MAKE VARS
.PHONY : clean cleanall forceall
.DEFAULT : all
.PRECIOUS : %.sh %.awk %.pl %.pm %.ps %.tgz %.gz \
%.rc %.gff %.gb %.fa README
.SECONDARY :
.SUFFIXES :
#
### INTERPRETERS
DATE = $(shell date)
USER = $(shell whoami)
GAWK = $(firstword $(shell which gawk))
GAWKV = $(shell $(GAWK) --version | \
$(GAWK) '$$0 ~ /^GNU Awk/ { print $$0; }')
BASH = $(firstword $(shell which bash))
BASHV = $(shell $(BASH) --version | \
$(GAWK) '$$0 ~ /^GNU bash/ { print $$0; }')
PERL = $(firstword $(shell which perl))
PERLV = $(shell $(PERL) --version | \
$(GAWK) '$$0 ~ /^This/ { \
gsub(/^This is perl,[ \t]+/,"",$$0); \
print $$0; \
}') #'
#
### COMMANDS
# You can update the following paths to your system settings
V = -v
RM = $(firstword $(shell which rm )) $(V)
RD = $(firstword $(shell which rmdir)) $(V)
CP = cp -v
MV = $(firstword $(shell which mv )) $(V)
LN = $(firstword $(shell which ln )) $(V)
MD = $(firstword $(shell which mkdir)) $(V)
CHM = $(firstword $(shell which chmod)) -c
CHO = $(firstword $(shell which chown)) -c
#
### LOCAL PATHS
WORK = .
SRC = $(WORK)/src
BIN = $(WORK)/bin
#
### LOCAL VARS
BINEXT = .sh .awk .pl .pm
GFF2APLOT = gff2aplot.pl
PARSEBLAST = parseblast.pl
BLAT2GFF = blat2gff.pl
SIM2GFF = sim2gff.pl
ALI2GFF = ali2gff
ALI2GFFD = $(SRC)/ali2gff
SRCCODE = $(GFF2APLOT) $(PARSEBLAST) \
$(BLAT2GFF) $(SIM2GFF) $(ALI2GFF)
BINCODE = $(addprefix $(BIN)/, $(SRCCODE))
#
### MAKE RULES
all: header main trailer
test :
@echo "### SORRY !!! Tests were not implemented yet...";
install : header installbin trailer
forceall : header cleanbin main trailer
clean : header cleanbin trailer
cleanall : header cleanbin trailer
cleanbin :
-@$(RM) -f $(wildcard $(BIN)/*);
main : $(BINCODE)
@$(CHM) 755 $^;
installbin : $(BINCODE)
@echo "### COPYING BIN FILES TO $(INSTALLDIR)...";
@$(CP) -p $^ $(INSTALLDIR)/;
#
### FINISHING CODE
$(addprefix $(BIN)/, $(ALI2GFF)) : $(addprefix $(ALI2GFFD)/, $(ALI2GFF))
mkdir -p $(BIN)
cp $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \
$(addprefix $(BIN)/, $(ALI2GFF))
$(addprefix $(ALI2GFFD)/, $(ALI2GFF)) : $(addprefix $(addprefix $(ALI2GFFD)/, $(ALI2GFF)), .h .c)
@echo "### Making ALI2GFF..."
@cd $(ALI2GFFD); \
$(MAKE) -f ./Makefile;
$(addprefix $(BIN)/, %.sh) : $(addprefix $(SRC)/, %.sh)
@echo "### Finishing BASH script from \"$<\" -> \"$@\"" ;
@( echo "#!$(BASH)"; cat $< ) > $@;
$(addprefix $(BIN)/, %.awk) : $(addprefix $(SRC)/, %.awk)
@echo "### Finishing GAWK script from \"$<\" -> \"$@\"" ;
@( echo "#!$(GAWK) -f"; cat $< ) > $@;
$(addprefix $(BIN)/, %.pl) : $(addprefix $(SRC)/, %.pl)
@echo "### Finishing PERL script from \"$<\" -> \"$@\"" ;
@( echo "#!$(PERL) -w"; cat $< ) > $@;
$(addprefix $(BIN)/, %.pm) : $(addprefix $(SRC)/, %.pm)
@echo "### Finishing PERL module from \"$<\" -> \"$@\"" ;
@$(CP) -u $< $@ ;
isexec : $(BINCODE)
@$(CHM) 755 $<;
#
### INFO RULES
info : header getinfo trailer
getinfo :
@echo "### BASH ### $(BASH) ### $(BASHV)";
@echo "### GAWK ### $(GAWK) ### $(GAWKV)";
@echo "### PERL ### $(PERL) ### $(PERLV)";
header :
@echo "###";
@echo "### RUNNING MAKEFILE";
@echo "###";
@echo "### $(DATE) -- $(USER)";
@echo "###";
trailer :
@echo "###";
@echo "### MAKEFILE DONE...";
@echo "###";
|
