-
Notifications
You must be signed in to change notification settings - Fork 108
/
configure.ac
349 lines (311 loc) · 10.3 KB
/
configure.ac
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
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
AC_PREREQ(2.62)
AC_INIT(ABySS, 2.3.10, [email protected], abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AC_CONFIG_MACRO_DIR([m4])
m4_include(m4/m4_ax_pthread.m4)
m4_include([m4/ax_cxx_compile_stdcxx.m4])
AX_CXX_COMPILE_STDCXX(11, noext, mandatory)
AM_INIT_AUTOMAKE(1.9.6 tar-ustar foreign subdir-objects)
AC_CONFIG_SRCDIR([ABYSS/abyss.cc])
AC_CONFIG_HEADERS([config.h])
# Checks for programs.
AC_PROG_AWK
AC_PROG_CC
AC_PROG_CPP
AC_PROG_CXX
AC_PROG_INSTALL
AC_PROG_RANLIB
AC_CHECK_TOOL(GHC, ghc)
AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
AC_CHECK_PROG(PANDOC, pandoc, yes)
AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
AM_PROG_AR
# Checks for header files.
AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
stddef.h stdint.h stdlib.h sys/param.h])
AC_HEADER_STDBOOL
# Checks for typedefs, structures, and compiler characteristics.
AC_C_BIGENDIAN
AC_C_CONST
AC_C_INLINE
AC_CHECK_TYPES([ptrdiff_t])
AC_TYPE_MODE_T
AC_TYPE_PID_T
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_INT64_T
AC_TYPE_UINT8_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
# Check for std::hash and std::tr1::hash.
AC_LANG_PUSH([C++])
AC_CHECK_TYPE([std::hash<int>],
AC_DEFINE(HAVE_STD_HASH, [1],
[Define if the system provides std::hash]),
[], [
#ifdef __FUJITSU
#include <string>
#else
#include <functional>
#endif])
AC_CHECK_TYPE([std::tr1::hash<int>],
AC_DEFINE(HAVE_STD_TR1_HASH, [1],
[Define if the system provides std::tr1::hash]),
[], [#include <tr1/functional>])
AC_CHECK_TYPE([std::tr1::tuple<int>],
AC_DEFINE(HAVE_STD_TR1_TUPLE, [1],
[Define if the system provides std::tr1::tuple]),
[], [#include <tr1/tuple>])
if test "x$ac_cv_type_std__tr1__tuple_int_" = "xyes"; then
# Avoid double-declaration of std::tr1::tuple by boost.
# See http://stackoverflow.com/questions/1156003/c-namespace-collision-with-gtest-and-boost
# for explanation.
AC_DEFINE(BOOST_HAS_TR1_TUPLE, [1],
[Define to disable declaration of std::tr1::tuple by boost])
fi
AM_CONDITIONAL([HAVE_TR1_TUPLE], [test x"$ac_cv_type_std__tr1__tuple_int_" = x"yes"])
AC_LANG_POP([C++])
# Checks for library functions.
AC_CHECK_FUNCS([dup2 gethostname getopt_long getpagesize \
memset strdup strerror strtoul])
AC_FUNC_FORK
AC_FUNC_MALLOC
AC_FUNC_MEMCMP
AC_FUNC_REALLOC
AC_FUNC_VPRINTF
# Checks for library constants.
AC_CHECK_DECL(HOST_NAME_MAX, [],
AC_DEFINE(HOST_NAME_MAX, [_POSIX_HOST_NAME_MAX],
[Define if the system does not provide HOST_NAME_MAX]),
[#include <limits.h>])
# Options to configure.
# Boost
AC_ARG_WITH(boost, AS_HELP_STRING([--with-boost=PATH],
[specify directory for the boost header files]))
if test "$with_boost" -a -d "$with_boost"; then
boost_cppflags="-isystem$with_boost -isystem$with_boost/include"
fi
# MPI
AC_ARG_WITH(mpi, AS_HELP_STRING([--with-mpi=PATH],
[specify prefix directory for the installed MPI parallel
computing library]))
if test "$with_mpi" -a -d "$with_mpi"; then
mpi_cppflags="-isystem$with_mpi/include"
if test -d "$with_mpi/lib64"; then
mpi_ldflags="-L$with_mpi/lib64"
else
mpi_ldflags="-L$with_mpi/lib"
fi
fi
AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich],
[use MPICH (default is to use Open MPI)]))
AC_ARG_ENABLE(lammpi, AS_HELP_STRING([--enable-lammpi],
[use LAM/MPI (default is to use Open MPI)]))
# SQLite
AC_ARG_WITH(sqlite, AS_HELP_STRING([--with-sqlite=PATH],
[specify prefix directory for the installed sqlite library]))
if test "$with_sqlite" -a "$with_sqlite" != "no" -a -d "$with_sqlite"; then
sqlite_cppflags="-I$with_sqlite/include"
if test -d "$with_sqlite/lib64"; then
sqlite_ldflags="-L$with_sqlite/lib64 -lsqlite3"
else
sqlite_ldflags="-L$with_sqlite/lib -lsqlite3"
fi
fi
# SparseHash
AC_ARG_WITH(sparsehash, AS_HELP_STRING([--with-sparsehash=PATH],
[specify prefix directory for the installed sparsehash library]))
if test "$with_sparsehash" -a "$with_sparsehash" != "no" -a -d "$with_sparsehash" ; then
sparsehash_cppflags="-isystem$with_sparsehash/include"
sparsehash_ldflags="-L$with_sparsehash/lib"
fi
# btllib
AC_ARG_WITH(btllib, AS_HELP_STRING([--with-btllib=PATH],
[specify prefix directory for the installed sqlite library]))
if test "$with_btllib" -a "$with_btllib" != "no" -a -d "$with_btllib" ; then
btllib_cppflags="-isystem$with_btllib/include"
btllib_ldflags="-L$with_btllib/lib"
fi
AC_ARG_ENABLE(fm, AS_HELP_STRING([--enable-fm],
[specify the width of the FM-index in bits (default is 64-bit)]),
[], [enable_fm=64])
AC_DEFINE_UNQUOTED(FMBITS, $enable_fm,
[Width of bits of the FM-index in bits])
AC_ARG_ENABLE(maxk, AS_HELP_STRING([--enable-maxk=N],
[set the maximum k-mer length (default is 192)]),
[], [enable_maxk=192])
AC_DEFINE_UNQUOTED(MAX_KMER, [$enable_maxk], [maximum k-mer length])
AC_ARG_ENABLE(max-hashes, AS_HELP_STRING([--enable-max-hashes],
[set the maximum number of Bloom filter hash functions (default is 32)]),
[], [enable_max_hashes=32])
AC_DEFINE_UNQUOTED(MAX_HASHES, [$enable_max_hashes], [maximum Bloom filter hash functions])
# Find the absolute path to the source.
my_abs_srcdir=$(cd $srcdir; pwd)
# Set compiler flags.
boost_ver=1.56.0
boost_ver_dir=boost_1_56_0
AC_SUBST(CPPFLAGS,
"-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $sqlite_cppflags $sparsehash_cppflags $btllib_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")
AC_SUBST(LDFLAGS, "$mpi_ldflags $sqlite_ldflags $sparsehash_ldflags $btllib_ldflags $LDFLAGS")
# Check for pthread.h / libpthread
# (optional 'make check' dependency)
AX_PTHREAD([have_pthread="yes"])
AM_CONDITIONAL([HAVE_PTHREAD], [test x"$have_pthread" = x"yes"])
# Check for the MPI parallel computing library.
libs="$LIBS"
AC_DEFINE(MPICH_SKIP_MPICXX, 1,
[Define to disable MPICH C++ bindings])
AC_DEFINE(OMPI_SKIP_MPICXX, 1,
[Define to disable OpenMPI C++ bindings])
AC_CHECK_HEADERS([mpi.h])
if test "$enable_mpich"; then
AC_CHECK_LIB([pthread], [pthread_create])
AC_CHECK_LIB([mpl], [MPL_env2int])
AC_CHECK_LIB([mpich], [MPI_Init])
ac_cv_lib_mpi_MPI_Init=$ac_cv_lib_mpich_MPI_Init
elif test "$enable_lammpi"; then
AC_CHECK_LIB([pthread], [pthread_create])
AC_CHECK_LIB([dl], [dlopen])
AC_CHECK_LIB([lam], [lam_mutex_lock])
AC_CHECK_LIB([mpi], [MPI_Init])
AC_LANG_PUSH([C++])
AC_CHECK_LIB([lammpi++], [main])
AC_LANG_POP([C++])
else
AC_CHECK_LIB([mpi], [MPI_Init])
fi
AM_CONDITIONAL([HAVE_LIBMPI],
[test $ac_cv_header_mpi_h = yes -a $ac_cv_lib_mpi_MPI_Init = yes])
AC_SUBST(MPI_LIBS, "$LIBS")
LIBS="$libs"
# Check for the math library.
AC_CHECK_LIB([m], [sqrt])
AC_CHECK_FUNCS([pow sqrt])
AC_CHECK_FUNC(ceilf, [], AC_DEFINE(ceilf, [ceil],
[Define if the system does not provide ceilf]))
# Check for the dynamic linking library.
AC_CHECK_LIB([dl], [dlsym])
# Check for popcnt instruction.
AC_COMPILE_IFELSE(
[AC_LANG_PROGRAM([[#include <stdint.h>],
[uint64_t x = 0;]],
[[__asm__("popcnt %1,%0" : "=r" (x) : "r" (x));]])],
[AC_DEFINE([HAVE_POPCNT], 1, [Define to 1 if you have popcnt.])],
[AC_DEFINE([HAVE_POPCNT], 0, [Define to 0 if you do not have popcnt.])])
# Check for the hash table implementation.
AC_LANG([C++])
AC_CHECK_HEADERS([ \
functional \
tr1/functional \
boost/functional/hash.hpp \
boost/property_map/property_map.hpp \
google/sparse_hash_map \
unordered_map tr1/unordered_map \
unordered_set tr1/unordered_set \
boost/unordered_set.hpp \
btllib/bloom_filter.hpp \
])
# Check for Boost.
if test $ac_cv_header_boost_property_map_property_map_hpp != yes; then
AC_MSG_ERROR([ABySS requires the Boost C++ libraries, which may
be downloaded from here: http://www.boost.org/users/download/
It is not necessary to compile Boost before installing it. The
following commands will download and install Boost for ABySS:
cd $my_abs_srcdir
wget http://downloads.sourceforge.net/project/boost/boost/$boost_ver/$boost_ver_dir.tar.bz2
tar jxf $boost_ver_dir.tar.bz2
cd -])
fi
# Check for SQLite
libs="$LIBS"
if test "$with_sqlite" != "no"; then
AC_CHECK_HEADERS([sqlite3.h])
AC_CHECK_LIB([sqlite3],[main])
fi
if (test "$ac_cv_header_sqlite3_h" = "yes" -a "$ac_cv_lib_sqlite3_main" = "yes"); then
AC_DEFINE(_SQL, 1, [Define to 1 if you have sqlite lib/header])
fi
AM_CONDITIONAL(HAVE_SQLITE3,
[test "$ac_cv_header_sqlite3_h" = "yes" -a "$ac_cv_lib_sqlite3_main" = "yes"],
[Define to 1 if you have sqlite lib/header])
AC_SUBST(SQLITE_LIBS, "$LIBS")
LIBS=$libs
# Check for OpenMP.
AC_OPENMP
if test -z $OPENMP_CXXFLAGS; then
OPENMP_CXXFLAGS=-Wno-unknown-pragmas
fi
# Check for btllib.
if test $ac_cv_header_btllib_bloom_filter_hpp != yes; then
AC_MSG_ERROR([ABySS requires the btllib C++ libraries, which may
be downloaded from here: https://github.com/bcgsc/btllib
It is necessary to compile btllib. The readme
in the GitHub repo contains instructs to compile btllib.])
fi
# Set compiler flags.
AC_ARG_ENABLE([werror], AS_HELP_STRING([--disable-werror],
[do not treat compiler warnings as errors]))
if test x"$enable_werror" = x"no"; then
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
elif test x"$enable_werror" = x"yes"; then
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
else
# default
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
fi
# Build abyss-paired-dbg and abyss-paired-dbg-mpi
AM_CONDITIONAL([PAIRED_DBG], [true])
AC_CONFIG_FILES([
Makefile
ABYSS/Makefile
Align/Makefile
Assembly/Makefile
Common/Makefile
DataLayer/Makefile
FMIndex/Makefile
Graph/Makefile
Parallel/Makefile
bin/Makefile
doc/Makefile
dialign/Makefile
kmerprint/Makefile
AdjList/Makefile
Konnector/Makefile
DAssembler/Makefile
DistanceEst/Makefile
Layout/Makefile
Map/Makefile
Overlap/Makefile
PopBubbles/Makefile
Scaffold/Makefile
SimpleGraph/Makefile
MergePaths/Makefile
KAligner/Makefile
PairedDBG/Makefile
ParseAligns/Makefile
PathOverlap/Makefile
Consensus/Makefile
FilterGraph/Makefile
GapFiller/Makefile
Sealer/Makefile
vendor/gtest-1.7.0/Makefile
RResolver/Makefile
Unittest/Makefile
LogKmerCount/Makefile
Bloom/Makefile
BloomDBG/Makefile
DataBase/Makefile
vendor/Makefile
])
if test "$with_sparsehash" != "no" -a "$ac_cv_header_google_sparse_hash_map" != "yes"; then
AC_MSG_ERROR([ABySS should be compiled with Google sparsehash to
reduce memory usage. It may be downloaded here:
https://github.com/sparsehash/sparsehash
If you do not wish to use sparsehash, specify --without-sparsehash.])
fi
if test x"$have_pthread" != x"yes"; then
AC_MSG_WARN([Warning: Running the unit tests with 'make check' has been disabled
because pthread.h and/or libpthread could not be found.])
fi
AC_OUTPUT