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|
define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
AC_INIT([tophat],[2.0.13],[tophat.cufflinks@gmail.com])
AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
AC_CONFIG_SRCDIR([config.h.in])
AC_CONFIG_HEADERS([config.h])
# AC_CONFIG_AUX_DIR([build-aux])
AM_INIT_AUTOMAKE
AC_ARG_VAR(PYTHON, [python program])
# Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
CXXFLAGS="$CXXFLAGS"
CFLAGS="$CFLAGS"
AC_PROG_CXX
AC_LANG([C++])
# AC_LANG([C])
m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
# Checks for programs.
AC_PROG_AWK
AC_PROG_CXX
AC_PROG_CC
AC_PROG_MAKE_SET
AC_PROG_RANLIB
AC_PROG_INSTALL
AM_PATH_PYTHON([2.4])
m4_include([ax_boost_base.m4])
m4_include([ax_boost_thread.m4])
# CXXFLAGS="$CXXFLAGS $threadLib"
AX_BOOST_BASE([1.38.0])
AX_BOOST_THREAD
if test -z "$BOOST_THREAD_LIBS"; then
AC_MSG_ERROR([boost.thread not found. Aborting.])
fi
# BAM related:
ac_bam_path=samtools-0.1.18
BAM_LIB="-lbam"
BAM_LDFLAGS="-L./$ac_bam_path"
BAM_CPPFLAGS="-I./$ac_bam_path"
AC_SUBST(BAM_CPPFLAGS)
AC_SUBST(BAM_LDFLAGS)
AC_SUBST(BAM_LIB)
# Checks for header files.
AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
# Checks for header files.
AC_HEADER_STDC
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_PID_T
AC_TYPE_SIZE_T
AC_CHECK_TYPES([ptrdiff_t])
AC_C_CONST
AC_SYS_LARGEFILE
# Checks for libraries.
AC_CHECK_LIB([z], [gzread])
# Checks for library functions.
AC_FUNC_MALLOC
AC_CHECK_FUNCS([memset strdup strrchr strtol strsep])
# check the platform
AC_CANONICAL_HOST
# ---------------------------------------------------------------------
# Debug and profile
# ---------------------------------------------------------------------
# set CFLAGS and CXXFLAGS
#user_CFLAGS="${CXXFLAGS}"
user_CFLAGS=${CFLAGS}
generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
ext_CFLAGS=""
debug_CFLAGS=""
user_LDFLAGS="$LDFLAGS"
AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
[ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
AC_ARG_ENABLE([debug],
[AS_HELP_STRING([--enable-debug],
[enable debugging info (default is no)])],
[], [enable_debug=no])
AC_ARG_ENABLE([optim],
[AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
[set optimization level (default is 3)])],
[if test "x$enable_optim" = xyes; then enable_optim=3; fi],
[enable_optim=3])
AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])
AS_IF([test "x$enable_debug" = xyes],
[debug_CFLAGS="-DDEBUG"],
[debug_CFLAGS="-DNDEBUG"])
CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
CXXFLAGS="$CFLAGS"
CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
LDFLAGS="$BOOST_LDFLAGS $BAM_LDFLAGS $user_LDFLAGS"
AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
# makefiles to configure
AC_CONFIG_FILES([Makefile src/Makefile])
# make it happen
AC_OUTPUT
# dump some configuration confirmations
echo \
"
-- ${PACKAGE_STRING} Configuration Results --
C++ compiler: ${CXX} ${CXXFLAGS}
Linker flags: ${LDFLAGS}
BOOST libraries: ${BOOST_THREAD_LIBS}"
if test x"${GCC}" = x"yes" ; then
gcc_version=`${CC} --version | head -n 1`
echo " GCC version: ${gcc_version}"
else
gcc_version=''
fi
echo \
" Host System type: ${host}
Install prefix: ${prefix}
Install eprefix: ${exec_prefix}
See config.h for further configuration information.
Email <${PACKAGE_BUGREPORT}> with questions and bug reports.
"
if test x"${PYTHON}" = x":" || ! test -x "${PYTHON}"; then
echo "WARNING! python was not found and is required to run tophat"
echo " Please install python and point configure to the installed location"
fi
|
