Package list tigr-glimmer / 8c578fa
Several changes to build packages of Glimmer3 Andreas Tille 13 years ago
11 changed file(s) with 42 addition(s) and 629 deletion(s). Raw diff Collapse all Expand all
+0
-423
Makefile less more
0 # -*- makefile -*-
1 # just make headings for each thing and put the headings
2 # on the line for ALL
3 PROJECTDIR = .
4 BINDIR = $(PROJECTDIR)
5
6 CC = gcc
7 CPPC = g++
8 CFLAGS = -O3 -g -Wall
9 LDFLAGS = -lm
10
11
12 BINARIES = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs
13 DEPEND_FILES = *.cc *.c *.h
14 CLEANABLE_FILES = *.o *~ $(BINARIES)
15 CLEANABLE_FILES += debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1
16
17 ALL = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists \
18 tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs
19
20 .SUFFIXES: .cc .c
21
22 .c.o:
23 $(CC) $(CFLAGS) -c $*.c -o $*.o
24
25 .cc.o:
26 $(CPPC) $(CFLAGS) -c $*.cc -o $*.o
27
28 all: $(ALL)
29
30 tigr-adjust: adjust.o delcher.o
31 $(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
32
33 tigr-anomaly: anomaly.o delcher.o gene.o
34 $(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
35
36 tigr-build-icm: build-icm.o misc.o
37 $(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
38
39 tigr-check: check.o delcher.o
40 $(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
41
42 tigr-codon-usage: codon-usage.o delcher.o gene.o
43 $(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
44
45 tigr-compare-lists: compare-lists.o delcher.o
46 $(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
47
48 tigr-extract: extract.o delcher.o
49 $(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
50
51 tigr-generate: generate.o delcher.o gene.o
52 $(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
53
54 tigr-get-len: get-len.o delcher.o
55 $(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
56
57 tigr-get-putative: get-putative.o delcher.o
58 $(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
59
60 tigr-glimmer2: glimmer2.o delcher.o gene.o rnabin.o
61 $(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
62
63 tigr-long-orfs: long-orfs.o delcher.o gene.o
64 $(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
65
66 tigr-rnabin: rnabin.o delcher.o
67 $(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
68
69 depend:
70 makedepend $(DEPEND_FILES)
71
72 clean:
73 /bin/rm -f $(CLEANABLE_FILES)
74
75 # DO NOT DELETE THIS LINE -- make depend depends on it.
76
77 adjust.o: delcher.h /usr/include/stdio.h /usr/include/features.h
78 adjust.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
79 adjust.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
80 adjust.o: /usr/include/bits/typesizes.h /usr/include/libio.h
81 adjust.o: /usr/include/_G_config.h /usr/include/wchar.h
82 adjust.o: /usr/include/bits/wchar.h /usr/include/gconv.h
83 adjust.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
84 adjust.o: /usr/include/stdlib.h /usr/include/math.h
85 adjust.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
86 adjust.o: /usr/include/bits/mathcalls.h /usr/include/string.h
87 adjust.o: /usr/include/ctype.h /usr/include/endian.h
88 adjust.o: /usr/include/bits/endian.h /usr/include/limits.h
89 adjust.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
90 adjust.o: /usr/include/errno.h /usr/include/bits/errno.h
91 adjust.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
92 adjust.o: /usr/include/asm-generic/errno.h
93 adjust.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
94 adjust.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
95 anomaly.o: delcher.h /usr/include/stdio.h /usr/include/features.h
96 anomaly.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
97 anomaly.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
98 anomaly.o: /usr/include/bits/typesizes.h /usr/include/libio.h
99 anomaly.o: /usr/include/_G_config.h /usr/include/wchar.h
100 anomaly.o: /usr/include/bits/wchar.h /usr/include/gconv.h
101 anomaly.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
102 anomaly.o: /usr/include/stdlib.h /usr/include/math.h
103 anomaly.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
104 anomaly.o: /usr/include/bits/mathcalls.h /usr/include/string.h
105 anomaly.o: /usr/include/ctype.h /usr/include/endian.h
106 anomaly.o: /usr/include/bits/endian.h /usr/include/limits.h
107 anomaly.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
108 anomaly.o: /usr/include/errno.h /usr/include/bits/errno.h
109 anomaly.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
110 anomaly.o: /usr/include/asm-generic/errno.h
111 anomaly.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
112 anomaly.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
113 check.o: delcher.h /usr/include/stdio.h /usr/include/features.h
114 check.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
115 check.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
116 check.o: /usr/include/bits/typesizes.h /usr/include/libio.h
117 check.o: /usr/include/_G_config.h /usr/include/wchar.h
118 check.o: /usr/include/bits/wchar.h /usr/include/gconv.h
119 check.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
120 check.o: /usr/include/stdlib.h /usr/include/math.h
121 check.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
122 check.o: /usr/include/bits/mathcalls.h /usr/include/string.h
123 check.o: /usr/include/ctype.h /usr/include/endian.h
124 check.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h
125 check.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h
126 check.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
127 check.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
128 check.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
129 check.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
130 codon-usage.o: delcher.h /usr/include/stdio.h /usr/include/features.h
131 codon-usage.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
132 codon-usage.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
133 codon-usage.o: /usr/include/bits/typesizes.h /usr/include/libio.h
134 codon-usage.o: /usr/include/_G_config.h /usr/include/wchar.h
135 codon-usage.o: /usr/include/bits/wchar.h /usr/include/gconv.h
136 codon-usage.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
137 codon-usage.o: /usr/include/stdlib.h /usr/include/math.h
138 codon-usage.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
139 codon-usage.o: /usr/include/bits/mathcalls.h /usr/include/string.h
140 codon-usage.o: /usr/include/ctype.h /usr/include/endian.h
141 codon-usage.o: /usr/include/bits/endian.h /usr/include/limits.h
142 codon-usage.o: /usr/include/time.h /usr/include/bits/time.h
143 codon-usage.o: /usr/include/assert.h /usr/include/errno.h
144 codon-usage.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
145 codon-usage.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
146 codon-usage.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
147 codon-usage.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
148 codon-usage.o: gene.h
149 compare-lists.o: delcher.h /usr/include/stdio.h /usr/include/features.h
150 compare-lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
151 compare-lists.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
152 compare-lists.o: /usr/include/bits/typesizes.h /usr/include/libio.h
153 compare-lists.o: /usr/include/_G_config.h /usr/include/wchar.h
154 compare-lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h
155 compare-lists.o: /usr/include/bits/stdio_lim.h
156 compare-lists.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h
157 compare-lists.o: /usr/include/math.h /usr/include/bits/huge_val.h
158 compare-lists.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
159 compare-lists.o: /usr/include/string.h /usr/include/ctype.h
160 compare-lists.o: /usr/include/endian.h /usr/include/bits/endian.h
161 compare-lists.o: /usr/include/limits.h /usr/include/time.h
162 compare-lists.o: /usr/include/bits/time.h /usr/include/assert.h
163 compare-lists.o: /usr/include/errno.h /usr/include/bits/errno.h
164 compare-lists.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
165 compare-lists.o: /usr/include/asm-generic/errno.h
166 compare-lists.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
167 compare-lists.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
168 delcher.o: delcher.h /usr/include/stdio.h /usr/include/features.h
169 delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
170 delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
171 delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h
172 delcher.o: /usr/include/_G_config.h /usr/include/wchar.h
173 delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h
174 delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
175 delcher.o: /usr/include/stdlib.h /usr/include/math.h
176 delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
177 delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h
178 delcher.o: /usr/include/ctype.h /usr/include/endian.h
179 delcher.o: /usr/include/bits/endian.h /usr/include/limits.h
180 delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
181 delcher.o: /usr/include/errno.h /usr/include/bits/errno.h
182 delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
183 delcher.o: /usr/include/asm-generic/errno.h
184 delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
185 delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
186 extract.o: delcher.h /usr/include/stdio.h /usr/include/features.h
187 extract.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
188 extract.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
189 extract.o: /usr/include/bits/typesizes.h /usr/include/libio.h
190 extract.o: /usr/include/_G_config.h /usr/include/wchar.h
191 extract.o: /usr/include/bits/wchar.h /usr/include/gconv.h
192 extract.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
193 extract.o: /usr/include/stdlib.h /usr/include/math.h
194 extract.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
195 extract.o: /usr/include/bits/mathcalls.h /usr/include/string.h
196 extract.o: /usr/include/ctype.h /usr/include/endian.h
197 extract.o: /usr/include/bits/endian.h /usr/include/limits.h
198 extract.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
199 extract.o: /usr/include/errno.h /usr/include/bits/errno.h
200 extract.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
201 extract.o: /usr/include/asm-generic/errno.h
202 extract.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
203 extract.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
204 gene.o: delcher.h /usr/include/stdio.h /usr/include/features.h
205 gene.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
206 gene.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
207 gene.o: /usr/include/bits/typesizes.h /usr/include/libio.h
208 gene.o: /usr/include/_G_config.h /usr/include/wchar.h
209 gene.o: /usr/include/bits/wchar.h /usr/include/gconv.h
210 gene.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
211 gene.o: /usr/include/stdlib.h /usr/include/math.h
212 gene.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
213 gene.o: /usr/include/bits/mathcalls.h /usr/include/string.h
214 gene.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h
215 gene.o: /usr/include/limits.h /usr/include/time.h /usr/include/bits/time.h
216 gene.o: /usr/include/assert.h /usr/include/errno.h /usr/include/bits/errno.h
217 gene.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
218 gene.o: /usr/include/asm-generic/errno.h
219 gene.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
220 gene.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
221 generate.o: delcher.h /usr/include/stdio.h /usr/include/features.h
222 generate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
223 generate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
224 generate.o: /usr/include/bits/typesizes.h /usr/include/libio.h
225 generate.o: /usr/include/_G_config.h /usr/include/wchar.h
226 generate.o: /usr/include/bits/wchar.h /usr/include/gconv.h
227 generate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
228 generate.o: /usr/include/stdlib.h /usr/include/math.h
229 generate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
230 generate.o: /usr/include/bits/mathcalls.h /usr/include/string.h
231 generate.o: /usr/include/ctype.h /usr/include/endian.h
232 generate.o: /usr/include/bits/endian.h /usr/include/limits.h
233 generate.o: /usr/include/time.h /usr/include/bits/time.h
234 generate.o: /usr/include/assert.h /usr/include/errno.h
235 generate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
236 generate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
237 generate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
238 generate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
239 generate.o: icm.h
240 get-len.o: delcher.h /usr/include/stdio.h /usr/include/features.h
241 get-len.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
242 get-len.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
243 get-len.o: /usr/include/bits/typesizes.h /usr/include/libio.h
244 get-len.o: /usr/include/_G_config.h /usr/include/wchar.h
245 get-len.o: /usr/include/bits/wchar.h /usr/include/gconv.h
246 get-len.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
247 get-len.o: /usr/include/stdlib.h /usr/include/math.h
248 get-len.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
249 get-len.o: /usr/include/bits/mathcalls.h /usr/include/string.h
250 get-len.o: /usr/include/ctype.h /usr/include/endian.h
251 get-len.o: /usr/include/bits/endian.h /usr/include/limits.h
252 get-len.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
253 get-len.o: /usr/include/errno.h /usr/include/bits/errno.h
254 get-len.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
255 get-len.o: /usr/include/asm-generic/errno.h
256 get-len.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
257 get-len.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
258 get-putative.o: delcher.h /usr/include/stdio.h /usr/include/features.h
259 get-putative.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
260 get-putative.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
261 get-putative.o: /usr/include/bits/typesizes.h /usr/include/libio.h
262 get-putative.o: /usr/include/_G_config.h /usr/include/wchar.h
263 get-putative.o: /usr/include/bits/wchar.h /usr/include/gconv.h
264 get-putative.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
265 get-putative.o: /usr/include/stdlib.h /usr/include/math.h
266 get-putative.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
267 get-putative.o: /usr/include/bits/mathcalls.h /usr/include/string.h
268 get-putative.o: /usr/include/ctype.h /usr/include/endian.h
269 get-putative.o: /usr/include/bits/endian.h /usr/include/limits.h
270 get-putative.o: /usr/include/time.h /usr/include/bits/time.h
271 get-putative.o: /usr/include/assert.h /usr/include/errno.h
272 get-putative.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
273 get-putative.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
274 get-putative.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
275 get-putative.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
276 glimmer2.o: delcher.h /usr/include/stdio.h /usr/include/features.h
277 glimmer2.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
278 glimmer2.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
279 glimmer2.o: /usr/include/bits/typesizes.h /usr/include/libio.h
280 glimmer2.o: /usr/include/_G_config.h /usr/include/wchar.h
281 glimmer2.o: /usr/include/bits/wchar.h /usr/include/gconv.h
282 glimmer2.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
283 glimmer2.o: /usr/include/stdlib.h /usr/include/math.h
284 glimmer2.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
285 glimmer2.o: /usr/include/bits/mathcalls.h /usr/include/string.h
286 glimmer2.o: /usr/include/ctype.h /usr/include/endian.h
287 glimmer2.o: /usr/include/bits/endian.h /usr/include/limits.h
288 glimmer2.o: /usr/include/time.h /usr/include/bits/time.h
289 glimmer2.o: /usr/include/assert.h /usr/include/errno.h
290 glimmer2.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
291 glimmer2.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
292 glimmer2.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
293 glimmer2.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
294 glimmer2.o: icm.h
295 long-orfs.o: delcher.h /usr/include/stdio.h /usr/include/features.h
296 long-orfs.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
297 long-orfs.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
298 long-orfs.o: /usr/include/bits/typesizes.h /usr/include/libio.h
299 long-orfs.o: /usr/include/_G_config.h /usr/include/wchar.h
300 long-orfs.o: /usr/include/bits/wchar.h /usr/include/gconv.h
301 long-orfs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
302 long-orfs.o: /usr/include/stdlib.h /usr/include/math.h
303 long-orfs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
304 long-orfs.o: /usr/include/bits/mathcalls.h /usr/include/string.h
305 long-orfs.o: /usr/include/ctype.h /usr/include/endian.h
306 long-orfs.o: /usr/include/bits/endian.h /usr/include/limits.h
307 long-orfs.o: /usr/include/time.h /usr/include/bits/time.h
308 long-orfs.o: /usr/include/assert.h /usr/include/errno.h
309 long-orfs.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
310 long-orfs.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
311 long-orfs.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
312 long-orfs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
313 long-orfs.o: gene.h
314 rnabin.o: rnabin.h delcher.h /usr/include/stdio.h /usr/include/features.h
315 rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
316 rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
317 rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h
318 rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h
319 rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h
320 rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
321 rnabin.o: /usr/include/stdlib.h /usr/include/math.h
322 rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
323 rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h
324 rnabin.o: /usr/include/ctype.h /usr/include/endian.h
325 rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h
326 rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
327 rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h
328 rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
329 rnabin.o: /usr/include/asm-generic/errno.h
330 rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
331 rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
332 translate.o: delcher.h /usr/include/stdio.h /usr/include/features.h
333 translate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
334 translate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
335 translate.o: /usr/include/bits/typesizes.h /usr/include/libio.h
336 translate.o: /usr/include/_G_config.h /usr/include/wchar.h
337 translate.o: /usr/include/bits/wchar.h /usr/include/gconv.h
338 translate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
339 translate.o: /usr/include/stdlib.h /usr/include/math.h
340 translate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
341 translate.o: /usr/include/bits/mathcalls.h /usr/include/string.h
342 translate.o: /usr/include/ctype.h /usr/include/endian.h
343 translate.o: /usr/include/bits/endian.h /usr/include/limits.h
344 translate.o: /usr/include/time.h /usr/include/bits/time.h
345 translate.o: /usr/include/assert.h /usr/include/errno.h
346 translate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
347 translate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
348 translate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
349 translate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
350 build-icm.o: /usr/include/stdlib.h /usr/include/features.h
351 build-icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
352 build-icm.o: /usr/include/stdio.h /usr/include/bits/types.h
353 build-icm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
354 build-icm.o: /usr/include/libio.h /usr/include/_G_config.h
355 build-icm.o: /usr/include/wchar.h /usr/include/bits/wchar.h
356 build-icm.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h
357 build-icm.o: /usr/include/bits/sys_errlist.h /usr/include/math.h
358 build-icm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
359 build-icm.o: /usr/include/bits/mathcalls.h /usr/include/string.h
360 build-icm.o: /usr/include/ctype.h /usr/include/endian.h
361 build-icm.o: /usr/include/bits/endian.h /usr/include/unistd.h
362 build-icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
363 build-icm.o: build-icm.h misc.h
364 misc.o: /usr/include/stdlib.h /usr/include/features.h
365 misc.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
366 misc.o: /usr/include/stdio.h /usr/include/bits/types.h
367 misc.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
368 misc.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
369 misc.o: /usr/include/bits/wchar.h /usr/include/gconv.h
370 misc.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h misc.h
371 delcher.o: /usr/include/stdio.h /usr/include/features.h
372 delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
373 delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
374 delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h
375 delcher.o: /usr/include/_G_config.h /usr/include/wchar.h
376 delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h
377 delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
378 delcher.o: /usr/include/stdlib.h /usr/include/math.h
379 delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
380 delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h
381 delcher.o: /usr/include/ctype.h /usr/include/endian.h
382 delcher.o: /usr/include/bits/endian.h /usr/include/limits.h
383 delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
384 delcher.o: /usr/include/errno.h /usr/include/bits/errno.h
385 delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
386 delcher.o: /usr/include/asm-generic/errno.h
387 delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
388 delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
389 icm.o: delcher.h /usr/include/stdio.h /usr/include/features.h
390 icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
391 icm.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
392 icm.o: /usr/include/bits/typesizes.h /usr/include/libio.h
393 icm.o: /usr/include/_G_config.h /usr/include/wchar.h
394 icm.o: /usr/include/bits/wchar.h /usr/include/gconv.h
395 icm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
396 icm.o: /usr/include/stdlib.h /usr/include/math.h /usr/include/bits/huge_val.h
397 icm.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
398 icm.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
399 icm.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h
400 icm.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h
401 icm.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
402 icm.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
403 icm.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
404 icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
405 rnabin.o: delcher.h /usr/include/stdio.h /usr/include/features.h
406 rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
407 rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
408 rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h
409 rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h
410 rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h
411 rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
412 rnabin.o: /usr/include/stdlib.h /usr/include/math.h
413 rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
414 rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h
415 rnabin.o: /usr/include/ctype.h /usr/include/endian.h
416 rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h
417 rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
418 rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h
419 rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
420 rnabin.o: /usr/include/asm-generic/errno.h
421 rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
422 rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
44 DM-Upload-Allowed: yes
55 Uploaders: Steffen Moeller <moeller@debian.org>,
66 Andreas Tille <tille@debian.org>
7 Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs
7 Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs, quilt
88 Standards-Version: 3.7.3
99 Homepage: http://www.tigr.org/software/glimmer/
1010 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0
+0
-1
debian/dirs less more
0 usr/bin
0 README
1 ACKNOWLEDGEMENTS
2 changelog.gz
3 build-icm.readme
4 extract.readme
5 glimmer2.readme
6 long-orfs.readme
0 docs/notes.pdf
1 glim302notes.pdf
0 tigr-adjust usr/bin
1 tigr-anomaly usr/bin
2 tigr-build-icm usr/bin
3 tigr-check usr/bin
4 tigr-codon-usage usr/bin
5 tigr-compare-lists usr/bin
6 tigr-extract usr/bin
7 tigr-generate usr/bin
8 tigr-get-len usr/bin
9 tigr-get-putative usr/bin
10 tigr-glimmer2 usr/bin
11 tigr-long-orfs usr/bin
12 tigr-run-glimmer2 usr/bin
0 bin/* usr/bin
1 debian/tigr-run-glimmer3 usr/bin
0 --- /dev/null
1 +++ glimmer3.02/Makefile
2 @@ -0,0 +1,7 @@
3 +all:
4 + cd src; make
5 +
6 +clean:
7 + cd src; make clean
8 + rm -f bin/* lib/* obj/*
9 +
0 01_Makefile.patch
00 #!/usr/bin/make -f
1 # -*- makefile -*-
2 # Sample debian/rules that uses debhelper.
3 # GNU copyright 1997 to 1999 by Joey Hess.
4 #
5 # Modified to make a template file for a multi-binary package with separated
6 # build-arch and build-indep targets by Bill Allombert 2001
1 # debian/rules for ncbi-epcr using cdbs
2 # Andreas Tille <tille@debian.org>, GPL
73
8 # Uncomment this to turn on verbose mode.
9 #export DH_VERBOSE=1
10
11 .PHONY: clean
12
4 include /usr/share/cdbs/1/rules/patchsys-quilt.mk
135 include /usr/share/cdbs/1/rules/debhelper.mk
14 include /usr/share/cdbs/1/class/langcore.mk
15
16 # This has to be exported to make some magic below work.
17 export DH_OPTIONS
18
19 CFLAGS = -Wall -g -Wno-deprecated
20
21 ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
22 CFLAGS += -O0
23 else
24 CFLAGS += -O2
25 endif
26 ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
27 INSTALL_PROGRAM += -s
28 endif
29
30 package = tigr-glimmer
31
32 build:build-arch-stamp build-indep-stamp
33 build-arch-stamp::
34 dh_testdir
35 # Add here commands to compile the indep part of the package.
36 $(MAKE) all
37 ln -f run-glimmer2 tigr-run-glimmer2
38 touch build-indep-stamp
6 include /usr/share/cdbs/1/class/makefile.mk
397
408 MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 debian/tigr-long-orfs.1
419
4412 .sgml.1:
4513 docbook-to-man $< > $@
4614
47 build-indep: $(MANPAGES)
48 gzip -9c CHANGELOG > changelog.gz
49 touch build-indep
15 clean::
16 dh_clean $(MANPAGES) tigr-run-glimmer2
17 rm -f bin/* lib/* obj/*
5018
51 clean::
52 dh_testdir
53 dh_testroot
54 rm -f build-arch-stamp build-indep-stamp configure-stamp changelog.gz
55 # Add here commands to clean up after the build process.
56 -$(MAKE) clean
57 dh_clean $(MANPAGES) tigr-run-glimmer2
19 build/tigr-glimmer:: $(MANPAGES)
20 cd bin; for bin in `ls | grep -v "^tigr-"` ; do mv "$$bin" tigr-"$$bin" ; done
0 #!/bin/sh
1 echo "run Glimmer3"
2 clear
3 echo "Genome is " $1
4 echo "Find non-overlapping orfs in tmp.coord"
5 rm -f tmp.coord
6 tigr-long-orfs $1 | tigr-get-putative >tmp.coord
7 echo "Extract training sequences to tmp.train"
8 rm -f tmp.train
9 tigr-extract $1 tmp.coord >tmp.train
10 wc tmp.train
11 echo "Build interpolated context model in tmp.model"
12 rm -f tmp.model
13 tigr-build-icm <tmp.train >tmp.model
14 echo "Predict genes with Glimmer3 with coordinates in g3.coord"
15 rm -f g3.coord
16 tigr-glimmer3 $1 tmp.model | tigr-get-putative >g3.coord
+0
-121
delcher.h less more
0 // A. L. Delcher
1 //
2 // File: ANNOTATION/Glimmer/delcher.h
3 // Version: 2.03 3 Dec 2002
4 //
5 // Copyright (c) 2002 by Arthur Delcher, Steven Salzberg, Simon
6 // Kasif, and Owen White. All rights reserved. Redistribution
7 // is not permitted without the express written permission of
8 // the authors.
9 //
10 // Common generic routines.
11 //
12
13
14 #ifndef __DELCHER_H_INCLUDED
15 #define __DELCHER_H_INCLUDED
16
17
18 #include <stdio.h>
19 #include <stdlib.h>
20 #include <iostream>
21 #include <iomanip>
22 #include <fstream>
23 #include <math.h>
24 #include <string.h>
25 #include <ctype.h>
26 #include <limits.h>
27 #include <float.h>
28 #include <time.h>
29 #include <assert.h>
30 #include <errno.h>
31 #include <unistd.h>
32
33 using namespace std;
34
35 #define TRUE 1
36 #define FALSE 0
37 #ifndef EXIT_FAILURE
38 #define EXIT_FAILURE -1
39 #endif
40 #ifndef EXIT_SUCCESS
41 #define EXIT_SUCCESS 0
42 #endif
43
44
45 const int FASTA_WIDTH = 60;
46 // Max number of characters to print on a FASTA data line
47
48
49 const char * Commatize
50 (long int n);
51 void Fasta_Print
52 (FILE * fp, char * s, char * hdr);
53 void Fasta_Print_N
54 (FILE * fp, char * s, int n, char * hdr);
55 FILE * File_Open
56 (const char *, const char *);
57 double Percent
58 (double a, double b);
59 void * Safe_calloc
60 (size_t N, size_t Len, size_t line_num = 0);
61 void * Safe_malloc
62 (size_t Len, size_t line_num = 0);
63 void * Safe_realloc
64 (void * Q, size_t Len, size_t line_num = 0);
65
66
67 template <class DT>
68 DT Max (DT, DT);
69 template <class DT>
70 DT Min (DT, DT);
71 template <class DT>
72 void Swap (DT &, DT &);
73
74
75 template <class DT>
76 DT Max (DT A, DT B)
77
78 // Return the larger of A and B .
79
80 {
81 if (A > B)
82 return A;
83 else
84 return B;
85 }
86
87
88
89 template <class DT>
90 DT Min (DT A, DT B)
91
92 // Return the smaller of A and B .
93
94 {
95 if (A < B)
96 return A;
97 else
98 return B;
99 }
100
101
102
103 template <class DT>
104 void Swap (DT & A, DT & B)
105
106 // Swap the values in A and B .
107
108 {
109 DT Save;
110
111 Save = A;
112 A = B;
113 B = Save;
114
115 return;
116 }
117
118
119
120 #endif
+0
-17
run-glimmer2 less more
0 #!/bin/sh
1 echo "run Glimmer2"
2 clear
3 echo "Genome is " $1
4 echo "Find non-overlapping orfs in tmp.coord"
5 rm -f tmp.coord
6 tigr-long-orfs $1 | tigr-get-putative >tmp.coord
7 echo "Extract training sequences to tmp.train"
8 rm -f tmp.train
9 tigr-extract $1 tmp.coord >tmp.train
10 wc tmp.train
11 echo "Build interpolated context model in tmp.model"
12 rm -f tmp.model
13 tigr-build-icm <tmp.train >tmp.model
14 echo "Predict genes with Glimmer2 with coordinates in g2.coord"
15 rm -f g2.coord
16 tigr-glimmer2 $1 tmp.model | tigr-get-putative >g2.coord