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configure.ac
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configure.ac
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AC_PREREQ(2.62)
AC_INIT(ABySS, 2.1.5, abyss-users@bcgsc.ca, abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
m4_include(m4/m4_ax_pthread.m4)
AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)
AC_CONFIG_SRCDIR([ABYSS/abyss.cc])
AC_CONFIG_HEADER([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], ["$GHC" --version])
AC_CHECK_PROG(PANDOC, pandoc, yes)
AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
# 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
AC_HEADER_STDC
# 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_SETVBUF_REVERSED
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
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, $enable_fm,
[Width of bits of the FM-index in bits])
AC_ARG_ENABLE(maxk, AS_HELP_STRING([--enable-maxk=N],
[set the maximum k-mer length (default is 128)]),
[], [enable_maxk=128])
AC_DEFINE_UNQUOTED(MAX_KMER, [$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 $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")
AC_SUBST(LDFLAGS, "$mpi_ldflags $sqlite_ldflags $sparsehash_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 \
])
# 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 $OPENMP_CXXFLAGS; then
OPENMP_CXXFLAGS=-Wno-unknown-pragmas
fi
# Set compiler flags.
AC_ARG_ENABLE([werror], AS_HELP_STRING([--disable-werror],
[do not treat compiler warnings as errors]))
if test x"$enable_werror" = x"no"; then
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
elif test x"$enable_werror" = x"yes"; then
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
else
# default
AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
fi
# Build abyss-paired-dbg and abyss-paired-dbg-mpi
AM_CONDITIONAL([PAIRED_DBG], [true])
AC_CONFIG_FILES([
Makefile
ABYSS/Makefile
Align/Makefile
Assembly/Makefile
Common/Makefile
DataLayer/Makefile
FMIndex/Makefile
Graph/Makefile
Parallel/Makefile
bin/Makefile
doc/Makefile
dialign/Makefile
kmerprint/Makefile
AdjList/Makefile
Konnector/Makefile
DAssembler/Makefile
DistanceEst/Makefile
Layout/Makefile
Map/Makefile
Misc/Makefile
Overlap/Makefile
PopBubbles/Makefile
Scaffold/Makefile
SimpleGraph/Makefile
MergePaths/Makefile
KAligner/Makefile
PairedDBG/Makefile
ParseAligns/Makefile
PathOverlap/Makefile
Consensus/Makefile
FilterGraph/Makefile
GapFiller/Makefile
Sealer/Makefile
lib/gtest-1.7.0/Makefile
Unittest/Makefile
LogKmerCount/Makefile
Bloom/Makefile
BloomDBG/Makefile
DataBase/Makefile
lib/bloomfilter/Makefile
lib/nthash/Makefile
])
if test "$with_sparsehash" != "no" -a "$ac_cv_header_google_sparse_hash_map" != "yes"; then
AC_MSG_ERROR([ABySS should be compiled with Google sparsehash to
reduce memory usage. It may be downloaded here:
https://code.google.com/p/sparsehash/
If you do not wish to use sparsehash, specify --without-sparsehash.])
fi
if test x"$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