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# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_WITH_HTSLIB
#
# DESCRIPTION
#
# This macro checks whether HTSlib <http://www.htslib.org/> is installed
# or nearby, and adds a --with-htslib=DIR option to the configure script
# for specifying the location. It locates either an installation prefix
# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
# HTSlib is fast-moving and users may wish to use an in-development tree.
#
# Different checks occur depending on the --with-htslib argument given:
#
# With --with-htslib=DIR, checks whether DIR is a source tree or contains
# a working installation.
# By default, searches for a source tree (with a name matching htslib*)
# within or alongside $srcdir. Produces AC_MSG_ERROR if there are
# several equally-likely candidates. If there are none, checks for
# a working default installation.
# With --with-htslib=system, checks for a working default installation.
#
# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
# (which unfortunately may cause a "you should use literals" warning when
# autoconf is run).
#
# The following output variables are set by this macro:
#
# HTSDIR Directory containing HTSlib source tree
# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib
# HTSLIB_LDFLAGS Linker flags for linking with HTSlib
#
# The following shell variables may be defined:
#
# ax_cv_htslib Set to "yes" if HTSlib was found
# ax_cv_htslib_which Set to "source", "install", or "none"
#
# LICENSE
#
# Copyright (C) 2015 Genome Research Ltd
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 1
AC_DEFUN([AX_WITH_HTSLIB],
[AC_ARG_WITH([htslib],
[AS_HELP_STRING([--with-htslib=DIR],
[use the HTSlib source tree or installation in DIR])
dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING()
AS_HELP_STRING([--with-htslib=system],
[use only a system HTSlib installation])],
[], [with_htslib=search])
case $with_htslib in
yes|search)
AC_MSG_CHECKING([location of HTSlib source tree])
case $srcdir in
.) srcp= ;;
*) srcp=$srcdir/ ;;
esac
found=
for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
do
if test "$dir" = "--"; then
test -n "$found" && break
elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
found="${found}1"
HTSDIR=$dir
fi
done
if test -z "$found"; then
AC_MSG_RESULT([none found])
ax_cv_htslib_which=system
elif test "$found" = 1; then
AC_MSG_RESULT([$HTSDIR])
ax_cv_htslib_which=source
else
AC_MSG_RESULT([several directories found])
AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use])
fi
;;
no) ax_cv_htslib_which=none ;;
system) ax_cv_htslib_which=system ;;
*)
HTSDIR=$with_htslib
if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
ax_cv_htslib_which=source
else
ax_cv_htslib_which=install
fi
;;
esac
case $ax_cv_htslib_which in
source)
ax_cv_htslib=yes
HTSLIB_CPPFLAGS="-I$HTSDIR"
HTSLIB_LDFLAGS="-L$HTSDIR"
# We can't use a literal, because $HTSDIR is user-provided and variable
AC_CONFIG_SUBDIRS($HTSDIR)
;;
system)
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
ax_cv_htslib_which=install
HTSDIR=
HTSLIB_CPPFLAGS=
HTSLIB_LDFLAGS=
;;
install)
ax_saved_CPPFLAGS=$CPPFLAGS
ax_saved_LDFLAGS=$LDFLAGS
HTSLIB_CPPFLAGS="-I$HTSDIR/include"
HTSLIB_LDFLAGS="-L$HTSDIR/lib"
CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
HTSDIR=
CPPFLAGS=$ax_saved_CPPFLAGS
LDFLAGS=$ax_saved_LDFLAGS
;;
none)
ax_cv_htslib=no
;;
esac
AC_SUBST([HTSDIR])
AC_SUBST([HTSLIB_CPPFLAGS])
AC_SUBST([HTSLIB_LDFLAGS])])
|
