7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/configure.ac src/htslib/configure.ac deleted file mode 100644 index 27fa1f48ccf..00000000000 --- src/htslib/configure.ac +++ /dev/null @@ -1,192 +0,0 @@ -# Configure script for htslib, a C library for high-throughput sequencing data. -# -# Copyright (C) 2015 Genome Research Ltd. -# -# Author: John Marshall <jm18@sanger.ac.uk> -# -# 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([HTSlib], m4_esyscmd_s([make print-version]), - [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(hts.c) -AC_CONFIG_HEADERS(config.h) - -dnl Copyright notice to be copied into the generated configure script -AC_COPYRIGHT([Portions copyright (C) 2015 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 -AC_PROG_RANLIB - -need_crypto=no - -AC_ARG_WITH([irods], - [AS_HELP_STRING([[--with-irods[=DIR]]], - [use RodsAPIs library (in DIR) to support iRODS URLs])], - [case $withval in - no) irods=disabled ;; - yes) irods=enabled ;; - *) irods=enabled; IRODS_HOME=$withval ;; - esac], - [irods=disabled]) - -AC_ARG_ENABLE([libcurl], - [AS_HELP_STRING([--enable-libcurl], - [enable libcurl-based support for http/https/etc URLs])], - [], [enable_libcurl=no]) - -AC_ARG_ENABLE([plugins], - [AS_HELP_STRING([--enable-plugins], - [enable separately-compiled plugins for file access])], - [], [enable_plugins=no]) -AC_SUBST(enable_plugins) - -AC_ARG_WITH([plugin-dir], - [AS_HELP_STRING([--with-plugin-dir=DIR], - [plugin installation location [LIBEXECDIR/htslib]])], - [case $withval in - yes|no) AC_MSG_ERROR([no directory specified for --with-plugin-dir]) ;; - esac], - [with_plugin_dir='$(libexecdir)/htslib']) -AC_SUBST([plugindir], $with_plugin_dir) - -AC_ARG_WITH([plugin-path], - [AS_HELP_STRING([--with-plugin-path=PATH], - [default HTS_PATH plugin search path [PLUGINDIR]])], - [case $withval in - yes) AC_MSG_ERROR([no path specified for --with-plugin-path]) ;; - no) with_plugin_path= ;; - esac], - [with_plugin_path=$with_plugin_dir]) -AC_SUBST([pluginpath], $with_plugin_path) - -dnl FIXME This pulls in dozens of standard header checks -AC_FUNC_MMAP -AC_CHECK_FUNCS(gmtime_r) - -if test $enable_plugins != no; then - AC_SEARCH_LIBS([dlopen], [dl], [], - [AC_MSG_ERROR([dlopen() not found - -Plugin support requires dynamic linking facilities from the operating system. -Either configure with --disable-plugins or resolve this error to build HTSlib.])]) - # TODO Test whether this is required and/or needs tweaking per-platform - LDFLAGS="$LDFLAGS -rdynamic" - AC_DEFINE([ENABLE_PLUGINS], 1, [Define if HTSlib should enable plugins.]) -fi - -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 - -HTSlib uses compression routines from the zlib library <http://zlib.net>. -Building HTSlib 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 HTSlib successfully.]) -fi - -if test $irods = enabled; then - # TODO Also test whether we require libgssapi_krb5 and AC_CHECK_LIB it - save_LDFLAGS=$LDFLAGS - LDFLAGS="$LDFLAGS -L$IRODS_HOME/lib/core/obj" - AC_CHECK_LIB([RodsAPIs], [getRodsEnvFileName], - [case $with_irods in - yes) define_IRODS_HOME='# Uses $(IRODS_HOME) from the environment' ;; - *) define_IRODS_HOME="IRODS_HOME = $with_irods" ;; - esac], - [AC_MSG_ERROR([iRODS development files not found - -Support for iRODS URLs requires the libRodsAPI client library and headers. -Configure with --with-irods=DIR (or just --with-irods if \$IRODS_HOME has -been exported with a suitable value), where DIR is the base of an iRODS tree -such that the library is present as DIR/lib/core/obj/libRodsAPI.* and headers -are present under DIR/lib/api/include and so on.])], - [-lgssapi_krb5 -lpthread]) - LDFLAGS=$save_LDFLAGS - AC_DEFINE([HAVE_IRODS], 1, [Define to 1 if iRODS file access is enabled.]) -else - define_IRODS_HOME='IRODS_HOME ?= /disabled' -fi -AC_SUBST([irods]) -AC_SUBST([define_IRODS_HOME]) - -libcurl=disabled -if test "$enable_libcurl" != no; then - AC_CHECK_LIB([curl], [curl_easy_pause], - [AC_DEFINE([HAVE_LIBCURL], 1, [Define if libcurl file access is enabled.]) - libcurl=enabled], - [AC_CHECK_LIB([curl], [curl_easy_init], - [message="library is too old (7.18+ required)"], - [message="library not found"]) - case "$enable_libcurl" in - check) AC_MSG_WARN([libcurl not enabled: $message]) ;; - *) AC_MSG_ERROR([libcurl $message - -Support for HTTPS and other SSL-based URLs requires routines from the libcurl -library <http://curl.haxx.se/libcurl/>. Building HTSlib with libcurl enabled -requires libcurl development files to be installed on the build machine; you -may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on -Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions) -is installed. - -Either configure with --disable-libcurl or resolve this error to build HTSlib.]) - ;; - esac]) - need_crypto=yes -fi -AC_SUBST([libcurl]) - -CRYPTO_LIBS= -if test $need_crypto != no; then - AC_CHECK_FUNC([CCHmac], - [AC_DEFINE([HAVE_COMMONCRYPTO], 1, - [Define if you have the Common Crypto library.])], - [save_LIBS=$LIBS - AC_SEARCH_LIBS([HMAC], [crypto], - [AC_DEFINE([HAVE_HMAC], 1, [Define if you have libcrypto-style HMAC().]) - case "$ac_cv_search_HMAC" in - -l*) CRYPTO_LIBS=$ac_cv_search_HMAC ;; - esac], - [AC_MSG_ERROR([SSL development files not found - -Support for AWS S3 URLs requires routines from an SSL library. Building -HTSlib with libcurl enabled requires SSL development files to be installed -on the build machine; you may need to ensure a package such as libgnutls-dev, -libnss3-dev, or libssl-dev (on Debian or Ubuntu Linux, corresponding to the -libcurl4-*-dev package installed) or similar on RPM-based Linux distributions. - -Either configure with --disable-libcurl or resolve this error to build HTSlib.])]) - LIBS=$save_LIBS]) -fi -AC_SUBST([CRYPTO_LIBS]) - -AC_CONFIG_FILES(config.mk) -AC_OUTPUT