# Configure script for bcftools, utilities for VCF/BCF files. # # Copyright (C) 2015,2017-2020 Genome Research Ltd. # # Author: John Marshall # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. dnl Process this file with autoconf to produce a configure script AC_INIT([BCFtools], [@PORTVERSION@], [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER AC_CONFIG_SRCDIR([main.c]) AC_CONFIG_HEADERS([config.h]) m4_include([m4/ax_with_htslib.m4]) m4_include([m4/hts_prog_cc_warnings.m4]) dnl Copyright notice to be copied into the generated configure script AC_COPYRIGHT([Portions copyright (C) 2015,2017-2020 Genome Research Ltd. This configure script is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.]) AC_PROG_CC dnl Turn on compiler warnings, if possible HTS_PROG_CC_WARNINGS dnl Flags to treat warnings as errors. These need to be applied to CFLAGS dnl later as they can interfere with some of the tests (notably AC_SEARCH_LIBS) HTS_PROG_CC_WERROR(hts_late_cflags) AC_SYS_LARGEFILE AC_ARG_ENABLE([bcftools-plugins], [AS_HELP_STRING([--disable-bcftools-plugins], [do not build optional plugins])], [], [enable_bcftools_plugins=yes]) AC_SUBST(enable_bcftools_plugins) AC_ARG_WITH([bcf-plugin-dir], [AS_HELP_STRING([--with-bcf-plugin-dir=DIR], [plugin installation location [LIBEXECDIR/bcftools]])], [case $withval in yes|no) AC_MSG_ERROR([no directory specified for --with-plugin-dir]) ;; esac], [with_bcf_plugin_dir='$(libexecdir)/bcftools']) AC_SUBST([bcf_plugindir], $with_bcf_plugin_dir) AC_ARG_WITH([bcf-plugin-path], [AS_HELP_STRING([--with-bcf-plugin-path=PATH], [default BCFTOOLS_PLUGINS plugin search path [PLUGINDIR]])], [case $withval in yes) AC_MSG_ERROR([no path specified for --with-bcf-plugin-path]) ;; no) with_bcf_plugin_path= ;; esac], [with_bcf_plugin_path=$with_bcf_plugin_dir]) AC_SUBST([bcf_pluginpath], $with_bcf_plugin_path) AC_ARG_ENABLE([perl-filters], [AS_HELP_STRING([--enable-perl-filters], [build in support for PERL scripts in -i/-e filtering expressions])], [], [enable_perl_filters=no]) AC_SUBST(enable_perl_filters) AC_ARG_ENABLE([libgsl], [AS_HELP_STRING([--enable-libgsl], [build options that require the GNU scientific library (changes bcftools license to GPL, see INSTALL for details)])], [], [enable_libgsl=no]) AC_ARG_WITH([cblas], [AS_HELP_STRING([--with-cblas], [which cblas library to use (only needed with libgsl; default: try cblas then gslcblas)])], [AS_CASE([$withval], [no],[AC_MSG_ERROR([no library name specified for --with-cblas])])], [with_cblas=yes]) AX_WITH_HTSLIB if test "$ax_cv_htslib" != yes; then AC_MSG_ERROR([HTSlib development files not found BCFtools uses HTSlib to parse bioinformatics file formats etc. Building it requires an unpacked HTSlib source tree (which will be built in conjunction with bcftools) or a previously-installed HTSlib. In either case you may need to configure --with-htslib=DIR to locate the appropriate HTSlib. FAILED. You must supply an HTSlib in order to build bcftools successfully.]) fi if test "$ax_cv_htslib_which" = source; then Hsource= Hinstall='#' else Hsource='#' Hinstall= fi AC_SUBST([Hsource]) AC_SUBST([Hinstall]) AS_IF([test "$enable_bcftools_plugins" != "no"], [dnl AC_MSG_CHECKING([shared library type]) test -n "$host_alias" || host_alias=unknown-`uname -s` AS_CASE([$host_alias], [*-cygwin* | *-CYGWIN*],[dnl host_result="Cygwin DLL" PLATFORM=CYGWIN PLUGIN_EXT=.cygdll HTSLIB_DLL=libhts.dll.a ], [*-msys* | *-MSYS* | *-mingw* | *-MINGW*],[dnl host_result="MSYS dll" PLATFORM=MSYS PLUGIN_EXT=.dll HTSLIB_DLL=hts.dll.a # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64, # %lld and %z printf formats work. It also enforces the snprintf to # be C99 compliant so it returns the correct values (in kstring.c). CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600"], [*-darwin* | *-Darwin*],[dnl host_result="Darwin dylib" PLATFORM=Darwin PLUGIN_EXT=.so], [*],[dnl host_result="plain .so" PLATFORM=default PLUGIN_EXT=.so]) AC_MSG_RESULT([$host_result]) AC_SUBST([PLATFORM]) AC_SUBST([PLUGIN_EXT]) AC_DEFINE_UNQUOTED([PLUGIN_EXT], ["$PLUGIN_EXT"], [Platform-dependent plugin filename extension.]) AC_SUBST([HTSLIB_DLL]) AC_DEFINE([ENABLE_BCF_PLUGINS], 1, [Define if BCFtools should enable plugins.]) AS_CASE([$PLUGIN_EXT], [*cygdll | *so], [AC_SEARCH_LIBS([dlopen], [dl], [], [AC_MSG_ERROR([dlopen() not found Plugin support requires dynamic linking facilities from the operating system. Either configure with --disable-bcftools-plugins or resolve this error to build bcftools.])])], [*dll], [AC_SEARCH_LIBS([LoadLibraryA], [], [], [AC_MSG_ERROR([LoadLibraryA() not found Plugin support requires dynamic linking facilities from the operating system. Either configure with --disable-bcftools-plugins or resolve this error to build bcftools.])])], ) AC_MSG_CHECKING([if the compiler accepts -rdynamic]) save_CFLAGS=$CFLAGS CFLAGS="$CFLAGS -rdynamic" AC_LINK_IFELSE([AC_LANG_PROGRAM()],[cc_rdynamic=yes],[cc_rdynamic=no]) CFLAGS=$save_CFLAGS AC_MSG_RESULT([$cc_rdynamic]) AS_IF([test "$cc_rdynamic" = "yes"],dnl [CC_RDYNAMIC_OPT=-rdynamic],[CC_RDYNAMIC_OPT=]) AC_SUBST([CC_RDYNAMIC_OPT]) ]) save_LIBS=$LIBS zlib_devel=ok dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) LIBS=$save_LIBS if test $zlib_devel != ok; then AC_MSG_ERROR([zlib development files not found BCFtools uses compression routines from the zlib library . Building bcftools requires zlib development files to be installed on the build machine; you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. FAILED. This error must be resolved in order to build bcftools successfully.]) fi AS_IF([test "$enable_libgsl" != "no"], [dnl gsl_devel=ok save_LIBS="$LIBS"dnl Libraries for GSL are listed in $(GSL_LIBS) GSL_LIBS= AC_CHECK_HEADER([gsl/gsl_version.h], [], [gsl_devel=missing], [;]) AS_IF([test "$gsl_devel" != "missing"], [dnl AS_CASE([$with_cblas], [yes],[AC_SEARCH_LIBS([cblas_dgemm],[cblas gslcblas], [GSL_LIBS="$ac_cv_search_cblas_dgemm"], [gsl_devel=missing])], [AC_CHECK_LIB([$with_cblas],[cblas_dgemm], [GSL_LIBS="-l$with_cblas"],[gsl_devel=missing])]) ]) AS_IF([test "$gsl_devel" != "missing"], [dnl AC_CHECK_LIB(gsl, gsl_multifit_gradient, [GSL_LIBS="-lgsl $GSL_LIBS"], [gsl_devel=missing], [$GSL_LIBS]) ]) AS_IF([test "$gsl_devel" != "ok"], [dnl AC_MSG_ERROR([libgsl development files not found The bcftools polysomy command uses routines from the GNU Scientific library . Building BCFtools with libgsl enabled requires libgsl development files to be installed on the build machine; you may need to ensure a package such as libgsl0-dev (on Debian or Ubuntu linux) or gsl-devel (on RPM-based Linux distributions) is installed. Either configure with --disable-libgsl or resolve this error to build bcftools. ]) ]) LIBS="$save_LIBS" USE_GPL=1 AC_SUBST([USE_GPL]) AC_SUBST([GSL_LIBS]) ]) AS_IF([test "$enable_perl_filters" != "no" ], [dnl save_LIBS="$LIBS" if ! perl -MExtUtils::Embed -e ccopts -e ldopts >/dev/null 2>&1; then AC_MSG_ERROR([Cannot `perl -MExtUtils::Embed -e ccopts -e ldopts`]) fi AC_DEFINE([ENABLE_PERL_FILTERS], 1, [Define if BCFtools should enable for support PERL scripts in -i/-e filtering expressions.]) PERL_CCOPTS="`perl -MExtUtils::Embed -e ccopts`" PERL_LIBS="`perl -MExtUtils::Embed -e ldopts`" dnl A hack to remove faulty "-arch i386" on mac as it breaks linking if test "x$PLATFORM" = "xDarwin"; then PERL_CCOPTS="`perl -MExtUtils::Embed -e ccopts | sed 's,-arch i386,,'`" PERL_LIBS="`perl -MExtUtils::Embed -e ldopts | sed 's,-arch i386,,'`" fi AC_SUBST([PERL_CCOPTS]) AC_SUBST([PERL_LIBS]) dnl Look for libperl AC_SEARCH_LIBS(Perl_call_pv, perl, [], [ AC_MSG_ERROR([Unable to find the Perl_call_pv() function for perl filters]) ],[$PERL_CCOPTS $PERL_LIBS]) LIBS="$save_LIBS" ]) dnl Apply value from HTS_PROG_CC_WERROR (if set) AS_IF([test "x$hts_late_cflags" != x],[CFLAGS="$CFLAGS $hts_late_cflags"]) dnl Look for regcomp in various libraries (needed on windows/mingw). AC_SEARCH_LIBS(regcomp, regex, [libregex=needed], []) dnl Force POSIX mode on Windows/Mingw test -n "$host_alias" || host_alias=unknown-`uname -s` case $host_alias in *-msys* | *-MSYS* | *-mingw* | *-MINGW*) host_result="MSYS dll" PLATFORM=MSYS PLUGIN_EXT=.dll # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64, # %lld and %z printf formats work. It also enforces the snprintf to # be C99 compliant so it returns the correct values (in kstring.c). CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600" ;; esac AC_CONFIG_FILES([config.mk]) AC_OUTPUT AS_IF([test "x$USE_GPL" != "x"], [dnl AC_MSG_NOTICE([License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ ])])