-
Notifications
You must be signed in to change notification settings - Fork 30
/
configure.ac
223 lines (185 loc) · 7.78 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
# configure.ac for LoFreq
AC_PREREQ(2.63)
# 2.60 needed for AC_USE_SYSTEM_EXTENSIONS
# 2.64 which allows to define a URL as well
# 2.68 seems to have updated ax_pthread
AC_INIT([LoFreq_Star], [2.1.5], [[email protected]])
# The AC_INIT macro can take any source file as an argument. It just
# checks that the file is there, which should, in turn, mean that the
# source directory is there. AC_INIT generates the following m4
# macros, output variables and preprocessor symbols:
AC_SUBST(PACKAGE_NAME)
AC_SUBST(PACKAGE_TARNAME)
AC_SUBST(PACKAGE_VERSION)
AC_SUBST(PACKAGE_STRING)
AC_SUBST(PACKAGE_BUGREPORT)
#AC_REVISION([m4_esyscmd_s([git describe --always --dirty])])
AC_REVISION([m4_esyscmd_s([git describe --always])])
# saves revision to configure
git_version=`git describe --always --dirty`
if test x"$git_version" = x; then
AC_DEFINE(GIT_VERSION, ["unknown"])
else
AC_DEFINE_UNQUOTED(GIT_VERSION, "$git_version")
fi
AC_MSG_NOTICE([Configuring $PACKAGE_NAME (version $PACKAGE_VERSION) for your system...
| ____|
| _ \ | __| _ \ _` |
| ( | __| | __/ ( |
_____| \___/ _| _| \___| \__, |
_|
])
#
# Created with http://patorjk.com/software/taag/#p=display&f=Shadow&t=LoFreq
# The AM_INIT_AUTOMAKE line adds several standard checks. This macro
# is always needed for automake. Obsolete: It takes the program name
# and version number as arguments.
AM_INIT_AUTOMAKE([foreign])
# This macro was introduced in Autoconf 2.60. If possible, enable
# extensions to C or Posix on hosts that normally disable the
# extensions.
AC_USE_SYSTEM_EXTENSIONS
# for cross compilation
#
AC_CANONICAL_HOST
## AC_CANONICAL_BUILD
## AC_CANONICAL_TARGET
# Set the @SET_MAKE@ variable=make if $(MAKE) not set
AC_PROG_MAKE_SET
# AC_PROG_RANLIB will allow you to build code in sub-directories into
# temporary libraries, which make will then link in with the rest of
# the code.
# AC_PROG_RANLIB rendered obsolte by LT_INIT?
AC_PROG_RANLIB
#
# disable-static: Need to disable static libraries, otherwise we can't
# link them into the dynamically loaded Python extension
#
#LT_INIT([disable-static])
# AC_PROG_INSTALL will generate an install target so that users may
# just type 'make install' to install the software.
AC_PROG_INSTALL
# check for C++ preprocessor and compiler and the library compiler
# (might change the compiler flags)
#
# Determine a C compiler to use. If using the GNU C compiler, set
# shell variable GCC to `yes'. If output variable CFLAGS was not
# already set, set it to `-g -O2' for the GNU C compiler (`-O2' on
# systems where GCC does not accept `-g'), or `-g' for other
# compilers.
# Note, optimization level can be overriden by user with env var
# CFLAGS
AC_PROG_CC
# Set output variable CPP to a command that runs the C preprocessor.
AC_PROG_CPP
# If the C compiler cannot compile ISO Standard C (currently C99),
# try to add an option to output variable `CC' to make it work. If
# the compiler does not support C99, fall back to supporting ANSI
# C89 (ISO C90).
# LoFreq: In theory we need for variadic macro support
# AC_PROG_CC_STDC
#
#If the C compiler is not in C99 mode by default, try to add an
#option to output variable `CC' to make it so. This macro tries
#various options that select C99 on some system or another,
#preferring extended functionality modes over strict conformance
#modes. It considers the compiler to be in C99 mode if it handles
#`_Bool', `//' comments, flexible array members, `inline', signed
#and unsigned `long long int', mixed code and declarations, named
#initialization of structs, `restrict', `va_copy', varargs macros,
#variable declarations in `for' loops, and variable length arrays.
#After calling this macro you can check whether the C compiler has
#been set to accept C99; if not, the shell variable
#`ac_cv_prog_cc_c99' is set to `no'.
AC_PROG_CC_C99
# safety check: AC_CONFIG_SRCDIR([src/clustal.h])
# Checks for standard header files.
# obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html
AC_HEADER_STDC
# Guess the next one is obsolete as well then?
# FIXME AC_CHECK_HEADERS(assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h)
# awk '/^#include *</ {print $2}' $(find src/ -name \*.[ch] -or -name \*.cpp) | grep -v argtable2.h | sort -u | tr -d '<>'
# Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_TYPE_SIZE_T
AC_C_INLINE
# Checks for library functions.
# AC_CHECK_FUNCS(strdup strstr strchr erand48)
# AW is there an automatic way to extract library functions used in the program?
# pthread support
#
AC_MSG_CHECKING([if we have pthreads support])
m4_include([m4/ax_pthread.m4])
AC_CONFIG_MACRO_DIR([m4])
AX_PTHREAD([
AC_DEFINE(HAVE_PTHREAD,1,[Define if you have POSIX threads libraries and header files.])
CLIBS="$PTHREAD_LIBS $LIBS"
CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
LDFLAGS="$LDFLAGS $PTHREAD_CFLAGS"
CC="$PTHREAD_CC"],
AC_MSG_ERROR([No pthread support on this machine]))
#AX_PTHREAD()
# if any of these sit in unusual places use
# export LDFLAGS="-L$path" before calling configure
AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm]))
AC_CHECK_LIB(z, gzread,, AC_MSG_ERROR([Could not find libz]))
AC_CHECK_LIB([gslcblas],[cblas_dgemm])
AC_CHECK_LIB(gsl, gsl_cdf_poisson_P,, AC_MSG_WARN([libgsl not found. Not using fast approximation]))
# http://www.gnu.org/software/automake/manual/html_node/Python.html
AM_PATH_PYTHON([2.7])
# argparse and a lot of other stuff is not available in 2.7
# on by default
AC_ARG_ENABLE([tools],
AS_HELP_STRING([--disable-tools], [Disable installation of tools]))
AM_CONDITIONAL(ENABLE_TOOLS, [test "x$enable_tools" != "xno"])
# --- debugging
#
AC_MSG_CHECKING([whether to build with debug information])
AC_ARG_ENABLE([debug],
[AS_HELP_STRING([--enable-debug],
[Enable debugging (default=no)])],
[debugit="$enableval"],
[debugit=no])
AC_MSG_RESULT([$debugit])
if test x"$debugit" = x"yes"; then
# User variables CFLAGS/CXXFLAGS are used last during compilation and
# can therefore overwrite system settings.
#
# if debugging was requested, add debugging info at the end of
# C[XX]FLAGS, which makes sure previous optimisation flags are
# overwritten (normally C[XX]FLAGS should not be modified as they
# are user variables):
# switch off assert etc
# AC_DEFINE([DEBUG],[],[Debug Mode])
CFLAGS="${CFLAGS} -O0 -pedantic"
CXXFLAGS="${CXXFLAGS} -O0 -pedantic"
else
# switch off assert etc
AC_DEFINE([NDEBUG],[],[No-debug Mode])
# Could set -O3 but that should be a user choice (env var CFLAGS)
fi
if test x"$HTSLIB" != x""; then
AC_MSG_ERROR([Use --with-htslib=/fullpath/to/htslibdir instead of HTSLIB variable])
fi
m4_include([m4/ax_with_htslib.m4])
AX_WITH_HTSLIB
if test "$ax_cv_htslib" != yes; then
AC_MSG_ERROR([HTSlib not found])
fi
AM_CONDITIONAL([HTSLIB_IS_SRC], [test "$ax_cv_htslib_which" = source])
AC_SUBST([AM_CFLAGS])
AC_SUBST([AM_LDFLAGS])
# AC_DEFINE([SOURCEQUAL_IGNORES_INDELS], [1], [ignore indels in SQ computation as long as we can't predict them])
#AC_ARG_ENABLE([alnerrprof],
# [AS_HELP_STRING([--enable-alnerrprof], [Enable use of alignment/mapping error profile (default=no)])],
# AC_DEFINE([USE_ALNERRPROF], [1], [support mapping error profile in LoFreq]))
AC_CONFIG_FILES(Makefile
src/cdflib90/Makefile
src/uthash/Makefile
src/lofreq/Makefile
src/scripts/Makefile
src/tools/setup_conf.py
src/tools/Makefile
)
AC_OUTPUT
AC_MSG_NOTICE([Done. Next, run 'make' to compile the source, followed by 'make install' to install it.])