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configure.ac
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configure.ac
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##########################################################################
# Setup
##########################################################################
# Autoconf initialistion. Sets package name version and contact details
AC_PREREQ([2.68])
AC_INIT([kat],[2.1.1],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
AC_CONFIG_SRCDIR([src/kat.cc])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_MACRO_DIR([m4])
AC_LANG_CPLUSPLUS
AC_PROG_CXXCPP
AC_PROG_CXX
AC_PROG_INSTALL
# Ensure there's C++11 support
AX_CXX_COMPILE_STDCXX_11(,[mandatory])
# Automake configuration.
AM_INIT_AUTOMAKE([1.11 subdir-objects foreign no-define tar-ustar])
AM_SILENT_RULES([yes])
m4_pattern_allow([AM_PROG_AR])
AM_PROG_AR
# Libtool setup
LT_INIT
# Detect OS
UNAME_S=`uname -s`
if test x"${UNAME_S}" == x"Linux"; then
AC_DEFINE([OS_LINUX], [1], [Linux detected])
fi
if test x"${UNAME_S}" == x"Darwin"; then
AC_DEFINE([OS_MAC], [1], [Mac detected])
fi
######################################################################
# Dependency checks
######################################################################
# Check some (almost) standard functionality is present that we require to run KAT.
#AC_CHECK_HEADER_STDBOOL # Commented this out because this was introduced after 2.63.
AC_FUNC_ERROR_AT_LINE
AC_FUNC_STRERROR_R
AC_TYPE_INT16_T
AC_TYPE_INT32_T
AC_TYPE_INT64_T
AC_TYPE_UINT8_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_TYPE_SIZE_T
AC_CHECK_FUNCS([floor])
AC_CHECK_FUNCS([memset])
AC_CHECK_FUNCS([sqrt])
AC_C_INLINE
AC_CHECK_HEADERS([string.h])
AC_CHECK_HEADERS([iostream])
AC_CHECK_HEADERS([stdio.h])
AC_CHECK_HEADERS([fstream])
AC_CHECK_HEADERS([memory])
AC_CHECK_HEADERS([vector])
AC_CHECK_HEADERS([glob.h])
# Check pthreads exists
AX_PTHREAD(, [AC_MSG_ERROR([pthreads lib not found. Please ensure that pthreads is properly built and configured.])])
# Required for Boost chrono on linux (clock_gettime). Doesn't exist on Mac
if test x"${UNAME_S}" != x"Darwin"; then
AC_SEARCH_LIBS([clock_gettime], [rt],
[RT_LIB="-lrt"],
[AC_MSG_ERROR([rt lib not found. Please ensure that rt is properly built and configured.])])
else
RT_LIB=""
fi
# Plotting
AC_ARG_ENABLE([gnuplot], AS_HELP_STRING([--enable-gnuplot], [Enable gnuplot plotting even if python matplotlib is available]), enable_gnuplot="yes", enable_gnuplot="no")
AM_PATH_PYTHON([], [], AC_MSG_ERROR([Python interpreter not found.]))
AX_PYTHON_DEVEL([>= '3.1'])
pymod_good="no"
if [[ -n "${PYTHON_VERSION}" ]]; then
if [[ -z "${PYTHON_EXTRA_LIBS}" ]]; then
pymod_good="no"
AC_MSG_WARN([Python3 detected but Python3 development library was not found. If you wish to use python plotting please install python3 library. e.g. "sudo apt-get install python3-dev" on debian systems.])
fi
pymod_good="yes"
AX_PYTHON_MODULE(numpy, ,python3)
if [[ "${PYMOD}" == "no" ]]; then
pymod_good="no"
fi
AX_PYTHON_MODULE(matplotlib, ,python3)
if [[ "${PYMOD}" == "no" ]]; then
pymod_good="no"
fi
AX_PYTHON_MODULE(scipy, ,python3)
if [[ "${PYMOD}" == "no" ]]; then
pymod_good="no"
fi
fi
# Check for gnuplot on path. Just emit a warning if not present
if [[ "${pymod_good}" == "no" ]] || [[ "${enable_gnuplot}" == "yes" ]]; then
AC_DEFINE([HAVE_PYTHON], [0], [Python not present])
AC_CHECK_PROG([gnuplot_found], [gnuplot], [yes], [no])
if [[ "${gnuplot_found}" == "no" ]] ; then
AC_DEFINE([HAVE_GNUPLOT], [0], [Gnuplot not present])
else
AC_DEFINE([HAVE_GNUPLOT], [1], [Gnuplot present])
fi
else
AC_DEFINE([HAVE_PYTHON], [1], [Python present])
fi
# Check for sphinx to build documentation (optional)
AC_CHECK_PROG([sphinx], [sphinx-build], [yes], [no])
if [[ "${sphinx}" == "yes" ]]; then
#Now check if the version is correct
sphinx_major_version=`sphinx-build --version 2>&1 | cut -d' ' -f3 | cut -d '.' -f 1 | tr -d " \t\n\r"`
sphinx_minor_version=`sphinx-build --version 2>&1 | cut -d' ' -f3 | cut -d '.' -f 2 | tr -d " \t\n\r"`
if [[ -z "${sphinx_major_version}" ]] ; then sphinx_major_version=0; fi
if [[ -z "${sphinx_minor_version}" ]] ; then sphinx_minor_version=0; fi
major_size=${#sphinx_major_version}
minor_size=${#sphinx_minor_version}
if (( ("${major_size}" > 2) || ("${minor_size}" > 2) )); then sphinx_major_version=0; sphinx_minor_version=0; fi
if (( ("${sphinx_major_version}" < 1 ) || ( ( "${sphinx_major_version}" >= 1 ) && ( "${sphinx_minor_version}" < 3 ) ) )); then
AC_MSG_WARN([Sphinx detected, but version is too old. Wont create documentation. You can still find the documentation online at: https://kat.readthedocs.org/en/latest/])
sphinx="no"
fi
else
AC_MSG_WARN([Sphinx not detected, wont create documentation. You can still find the documentation online at: https://kat.readthedocs.org/en/latest/])
fi
AM_CONDITIONAL([MAKE_DOCS], [test x$sphinx = xyes])
AC_SUBST([MAKE_DOCS])
## Check for boost
AX_BOOST_BASE([1.52],, [AC_MSG_ERROR([Boost not found. Please ensure that boost is properly built and the BOOST_ROOT environment variable is set. Alternatively you can override BOOST_ROOT with the --with-boost option.])])
AX_BOOST_FILESYSTEM
AX_BOOST_SYSTEM
AX_BOOST_PROGRAM_OPTIONS
AX_BOOST_CHRONO
AX_BOOST_TIMER
define([PC_FILE], lib/kat-2.1.pc)
# Combine BOOST variables (apart for BOOST_TEST)
BOOST_LIBS="${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} ${BOOST_SYSTEM_LIB} ${BOOST_TIMER_LIB}"
BOOST_STATIC_LIBS="${BOOST_TIMER_STATIC_LIB} ${BOOST_CHRONO_STATIC_LIB} ${RT_LIB} ${BOOST_FILESYSTEM_STATIC_LIB} ${BOOST_PROGRAM_OPTIONS_STATIC_LIB} ${BOOST_SYSTEM_STATIC_LIB} "
AC_SUBST([BOOST_STATIC_LIBS])
AM_CXXFLAGS="-DCPLUSPLUS"
AC_SUBST([AM_CXXFLAGS])
if [[ "${pymod_good}" == "yes" ]]; then
AM_CPPFLAGS="${BOOST_CPPFLAGS} ${PYTHON_CPPFLAGS}"
AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_STATIC_LIBS} ${PYTHON_EXTRA_LIBS} ${PYTHON_LIBS}"
AM_LDFLAGS="${BOOST_LDFLAGS} ${PYTHON_EXTRA_LDFLAGS}"
else
AM_CPPFLAGS="${BOOST_CPPFLAGS}"
AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_STATIC_LIBS}"
AM_LDFLAGS="${BOOST_LDFLAGS}"
fi
AC_SUBST([AM_CPPFLAGS])
AC_SUBST([AM_LDFLAGS])
AC_SUBST([AM_LIBS])
AC_CONFIG_HEADERS([config.h])
AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat-2.1.pc lib/Makefile src/Makefile tests/Makefile tests/compat.sh deps/seqan-library-2.0.0/Makefile])
AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
AC_OUTPUT
if [[ "${pymod_good}" == "yes" ]] && [[ "$enable_gnuplot" == "no" ]] ; then
AC_MSG_NOTICE([Using python plotting])
else
if [[ "${gnuplot_found}" == "yes" ]]; then
if [[ "$enable_gnuplot" == "no" ]]; then
AC_MSG_WARN([Python3, or some required python modules where not found. Python via matplotlib is the preferred plotting method in KAT. If you want to use python plotting (the preferred option) then we suggest you install anaconda3 (or python3 with numpy, scipy and matplotlib separately). However, gnuplot was detected so KAT plots will be generated via gnuplot instead.])
else
AC_MSG_NOTICE([Using gnuplot plotting])
fi
else
AC_MSG_WARN([Neither python (with plotting modules present) or Gnuplot not detected. KAT will still work (minus plots). Should you require plotting functionality, you must install either anaconda3 (or python3 with numpy, scipy and matplotlib) or gnuplot, and then reconfigure and compile to enable plotting in KAT.])
fi
fi
if [[ "${sphinx}" == "no" ]]; then
AC_MSG_WARN([Sphinx not detected, or version is too old. Wont create documentation. You can still find the documentation online at: https://kat.readthedocs.org/en/latest/])
else
AC_MSG_NOTICE([Building documentation with sphinx])
fi