-
Notifications
You must be signed in to change notification settings - Fork 0
/
Makefile.in
255 lines (220 loc) · 7.9 KB
/
Makefile.in
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
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
# Top level Makefile for HMMER3
#
# On most systems, to build H3 you should only need:
# % ./configure; make
#
# Optionally, you can run a test suite:
# % make check
#
# And optionally, you can install everything more permanently:
# % make install
#
# For more information, see the Installation chapter of the HMMER
# User's Guide.
#
# VPATH and shell configuration
#
top_srcdir = @top_srcdir@
srcdir = @srcdir@
VPATH = @srcdir@
SHELL = /bin/sh
# location of easel
ESLDIR = @HMMER_ESLDIR@
# location of libdivsufsort for suffix array creation
SADIR = @HMMER_SADIR@
# Package information
#
PACKAGE = @PACKAGE_NAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
# Installation targets
#
prefix = @prefix@
exec_prefix = @exec_prefix@
datarootdir = @datarootdir@
bindir = @bindir@
libdir = @libdir@
includedir = @includedir@
mandir = @mandir@
docdir = @docdir@
pdfdir = @pdfdir@
mandir = @mandir@
man1dir = ${mandir}/man1
man1ext = .1
# Compiler configuration
#
CC = @CC@
CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
LDFLAGS = -static @LDFLAGS@
SIMDFLAGS = @SIMD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
# Other tools
#
AR = @AR@
RANLIB = @RANLIB@
INSTALL = @INSTALL@
# beautification magic stolen from git
#
QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
QUIET_SUBDIR1 =
ifndef V
QUIET_CC = @echo ' ' CC $@;
QUIET_GEN = @echo ' ' GEN $@;
QUIET_AR = @echo ' ' AR $@;
QUIET_SUBDIR0 = +@subdir=
QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
${MAKE} -C $$subdir
endif
# Programs installed by HMMER (stable, documented)
#
PROGS = alimask\
hmmalign\
hmmbuild\
hmmconvert\
hmmemit\
hmmfetch\
hmmpress\
hmmscan\
hmmsearch\
hmmsim\
hmmstat\
jackhmmer\
phmmer\
nhmmer\
nhmmscan\
hmmpgmd
.PHONY: all dev check pdf install uninstall clean distclean TAGS
# all: Compile all documented executables.
# (Excludes test programs.)
#
all:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} all
# dev: compile all executables, including drivers.
#
dev:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} dev
# tests: compile all test drivers for 'make check'
#
tests:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
# check: Run test suites.
#
check:
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
# pdf: compile the User Guides.
#
pdf:
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
# install: installs the binaries in ${bindir}/
# When man pages are done, will install man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
# Creates these directories if they don't exist.
# Prefix those paths with ${DESTDIR} (rarely used, usually null;
# may be set on a make command line when building contrib RPMs).
install:
${INSTALL} -d ${DESTDIR}${bindir}
${INSTALL} -d ${DESTDIR}${libdir}
${INSTALL} -d ${DESTDIR}${includedir}
${INSTALL} -d ${DESTDIR}${man1dir}
${INSTALL} -d ${DESTDIR}${pdfdir}
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} install
# uninstall: Reverses the steps of "make install".
#
uninstall:
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} uninstall
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} uninstall
# "make clean" removes almost everything except configuration files.
#
clean:
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} clean
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
# "make distclean" leaves a pristine source distribution.
#
distclean:
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} distclean
-rm config.log config.status
-rm -rf autom4te.cache
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
-rm -f src/impl
-rm Makefile
#Use 'ifneq' instead of 'test -e' because the '+@' in QUIET_SUBDIR0 can't
#be passed to the shell. Note that ifneq breaks if indented.
ifneq (,$(wildcard ./release-notes/LICENSE.sh))
-rm -f release-notes/LICENSE.sh
endif
TAGS:
-rm -f ${top_srcdir}/TAGS
make tags-append
tags-append:
etags -o ${top_srcdir}/TAGS -a ${srcdir}/Makefile.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/COPYRIGHT
etags -o ${top_srcdir}/TAGS -a ${srcdir}/INSTALL
etags -o ${top_srcdir}/TAGS -a ${srcdir}/LICENSE
etags -o ${top_srcdir}/TAGS -a ${srcdir}/README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/configure.ac
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.pl
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.man
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/boilerplate-tail
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.tex
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/00README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/x-*
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/pmark-*
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pl
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sh
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pm
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sqc
${QUIET_SUBDIR0}easel ${QUIET_SUBDIR1} tags-append
################################################################
# HMMER - Biological sequence analysis with profile HMMs
# Version 3.1b2; February 2015
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Other copyrights also apply. See the COPYRIGHT file for a full list.
#
# HMMER is distributed under the terms of the GNU General Public License
# (GPLv3). See the LICENSE file for details.
#
# SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/Makefile.in $
# SVN $Id: Makefile.in 4489 2013-06-19 02:46:43Z wheelert $
################################################################