path: root/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild

# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

EAPI=5

inherit eutils flag-o-matic multilib toolchain-funcs

MY_TAG="Jun_15_2010"
MY_Y="${MY_TAG/*_/}"
MY_PV="9_0_0"
MY_P="ncbi_cxx--${MY_PV}"
#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz

DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"

LICENSE="public-domain"
SLOT="0"
IUSE="
	debug static-libs static threads pch
	test wxwidgets odbc
	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
	glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""

# sys-libs/db should be compiled with USE=cxx
DEPEND="
	berkdb? ( sys-libs/db:4.3[cxx] )
	ftds? ( dev-db/freetds )
	boost? ( dev-libs/boost )
	curl? ( net-misc/curl )
	sqlite? ( dev-db/sqlite )
	sqlite3? ( dev-db/sqlite:3 )
	mysql? ( virtual/mysql )
	gnutls? ( net-libs/gnutls )
	ssl? ( dev-libs/openssl )
	fltk? ( x11-libs/fltk )
	opengl? ( virtual/opengl )
	mesa? ( media-libs/mesa
		media-libs/glew
	)
	glut? ( media-libs/freeglut )
	freetype? ( media-libs/freetype )
	fastcgi? ( www-apache/mod_fastcgi )
	python? ( dev-lang/python )
	cppunit? ( dev-util/cppunit )
	icu? ( dev-libs/icu )
	expat? ( dev-libs/expat )
	sablotron? ( app-text/sablotron )
	xml? ( dev-libs/libxml2 )
	xslt? ( dev-libs/libxslt )
	xerces? ( dev-libs/xerces-c )
	xalan? ( dev-libs/xalan-c )
	muparser? ( dev-cpp/muParser )
	hdf5? ( sci-libs/hdf5 )
	gif? ( media-libs/giflib )
	jpeg? ( virtual/jpeg )
	png? ( media-libs/libpng )
	tiff? ( media-libs/tiff )
	xpm? ( x11-libs/libXpm )
	dev-libs/lzo
	app-arch/bzip2
	dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge


# seems muParser is required, also glew is required. configure exitss otherwise

RDEPEND="${DEPEND}"

S="${WORKDIR}/${MY_P}"

src_prepare() {
#	filter-ldflags -Wl,--as-needed
#	append-ldflags -Wl,--no-undefined
#	sed -i -e 's/-print-file-name=libstdc++.a//' \
#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
#		src/build-system/configure || die
#	epatch \
#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
#		"${FILESDIR}"/curl-types.patch \
#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
#		"${FILESDIR}"/report_project_settings_configure.patch \
#		"${FILESDIR}"/make_install.patch

#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch

#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch

#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"

	local PATCHES=(
		"${FILESDIR}"/${P}-conf-opts.patch
		"${FILESDIR}"/${P}-as-needed.patch
		"${FILESDIR}"/${P}-fix-creaders-linking.patch
		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
		"${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
		"${FILESDIR}"/${P}-remove-LZO-definition-upstream.patch
		)
	epatch ${PATCHES[@]}

	tc-export CXX CC

#	cd src/build-system || die
#	eaclocal -I.
#	eautoconf
}

src_configure() {
	local myconf=()
	#--without-optimization  turn off optimization flags in non-debug mode
	#--with-profiling        build profiled versions of libs and apps
	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
	#--with-plugin-auto-load always enable the plugin manager by default
	#--with-bundles          build bundles in addition to dylibs on Mac OS X
	#--with-bin-release      build executables suitable for public release
	#	no dll and such
	#--with-64               compile to 64-bit code
	#--with-universal        build universal binaries on Mac OS X
	#--with-universal=CPUs   build universal binaries targeting the given CPUs
	#--without-exe           do not build executables
	#--with-relative-runpath=P specify an executable-relative DLL search path
	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
	#--with-limited-linker   don't attempt to build especially large projects
	#--with-extra-action=    script to call after the configuration is complete
	#--with-autodep          automatic generation of dependencies (GNU make)
	#--with-fake-root=DIR    appear to have been built under DIR
	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
	#--without-execopy       do not copy built executables to the BIN area
	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
	#--with-lib-rebuilds=ask ask whether to update each app's libraries
	#--without-deactivation  keep old copies of libraries that no longer build
	#--without-makefile-auto-update  do not auto-update generated makefiles
	#--with-projects=FILE    build projects listed in FILE by default
	#--without-flat-makefile do not generate an all-encompassing flat makefile
	#--with-configure-dialog allow interactive flat makefile project selection
	#--with-saved-settings=F load configuration settings from the file F
	#--with-check-tools=...  use the specified tools for testing
	#--with-ncbi-public      ensure compatibility for all in-house platforms
	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
	#--without-ftds-renamed  do not rename Sybase DBLIB symbols in built-in FTDS
	#--without-sp            do not use SP libraries
	#--without-orbacus       do not use ORBacus CORBA libraries
	#--with-orbacus=DIR      use ORBacus installation in DIR
	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
	#--with-sablot=DIR       use Sablotron installation in DIR
	#--without-sablot,       do not use Sablotron
	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
	#--without-oechem        do not use OEChem
	#--with-sge=DIR          use Sun Grid Engine installation in DIR
	#--without-sge           do not use Sun Grid Engine
	#--with-magic=DIR        use libmagic installation in DIR
	#--without-magic         do not use libmagic
	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
	#--without-connext       do not build non-public CONNECT library extensions
	#--without-serial        do not build the serialization library and tools
	#--without-objects       do not generate/build serializeable objects from ASNs
	#--without-dbapi         do not build database connectivity libraries
	#--without-app           do not build standalone applications like ID1_FETCH
	#--without-gui           do not build most graphical projects
	#--without-algo          do not build CPU-intensive algorithms
	#--without-internal      do not build internal projects
	#--with-gbench           ensure that Genome Workbench can be built
	#--without-gbench        do not build Genome Workbench
	myconf+=(
	--with-dll
	--with-lfs
	--with-build-root="${S}"_build
	--without-suffix
	--without-hostspec
	--without-version
	--with-bincopy
	--without-strip
	--without-ccache
	--without-distcc
#	--with-ncbi-c
	--without-ctools
#	--with-sss
#	--with-sssutils
#	--with-sssdb
#	--with-included-sss
	--with-z="${EPREFIX}/usr"
	--with-bz2="${EPREFIX}/usr"
	--with-muparser="${EPREFIX}/usr"
	--without-sybase
	--with-autodep

# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
# ./configure ... --with-flat-makefile
# cd .../build
# make -f Makefile.flat
#
	--with-flat-makefile
#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs


# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc
	$(use_with debug)
	$(use_with debug max-debug)
	$(use_with debug symbols)
	$(use_with static-libs static)
	$(use_with static static-exe)
	$(use_with threads mt)
	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
	$(use_with test check)
	$(use_with pch)
	$(use_with lzo lzo "${EPREFIX}/usr")
	$(use_with pcre pcre "${EPREFIX}/usr")
	$(use_with gnutls gnutls "${EPREFIX}/usr")
	$(use_with ssl openssl "${EPREFIX}/usr")
	$(use_with ftds ftds "${EPREFIX}/usr")
	$(use_with mysql mysql "${EPREFIX}/usr")
	$(use_with fltk fltk "${EPREFIX}/usr")
	$(use_with opengl opengl "${EPREFIX}/usr")
	$(use_with mesa mesa "${EPREFIX}/usr")
	$(use_with opengl glut "${EPREFIX}/usr")
	$(use_with opengl glew "${EPREFIX}/usr")
	$(use_with opengl glew-mx)
	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
	$(use_with wxwidgets wxwidgets-ucs)
	$(use_with freetype freetype "${EPREFIX}/usr")
	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
	$(use_with berkdb bdb "${EPREFIX}/usr")
	$(use_with odbc odbc "${EPREFIX}/usr")
	$(use_with python python "${EPREFIX}/usr")
	$(use_with boost boost "${EPREFIX}/usr")
	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
	$(use_with icu icu "${EPREFIX}/usr")
	$(use_with expat expat "${EPREFIX}/usr")
	$(use_with xml libxml "${EPREFIX}/usr")
	$(use_with xml libxslt "${EPREFIX}/usr")
	$(use_with xerces xerces "${EPREFIX}/usr")
	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
	$(use_with xalan xalan "${EPREFIX}/usr")
#	$(use_with gif gif "${EPREFIX}/usr")
	$(use_with jpeg jpeg "${EPREFIX}/usr")
	$(use_with tiff tiff "${EPREFIX}/usr")
	$(use_with png png "${EPREFIX}/usr")
	$(use_with xpm xpm "${EPREFIX}/usr")
	$(use_with curl curl "${EPREFIX}/usr")
#	$(use_with X x "${EPREFIX}/usr")
	$(use_with X x)
	)

	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )

	# TODO
	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9

	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"

#	bash \
#		./src/build-system/configure \
#	cd src/build-system || die
	econf \
		--srcdir="${S}" \
		--prefix="${EPREFIX}/usr" \
		--libdir=/usr/lib64 \
		${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \
		${myconf[@]} || die
#--without-debug \
#		--with-bin-release \
#		--with-bincopy \
#		--without-static \
#		--with-dll \
#		--with-mt \
#		--with-lfs \
#		--prefix="${ED}"/usr \
#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
#		|| die
#	econf ${myconf[@]}
}

src_compile() {
	# all_r would ignore the --with-projects contents and build more
	# emake all_r -C GCC*-Release*/build || die
	# all_p with compile only selected/required components
#	cd "${S}"_build &&\

    # disabling this because we need to take the flat Makefile route
	# emake all_p -C "${S}"_build/build

	# take the flat Makefile route
	emake -f Makefile.flat -C "${S}"_build/build


#	emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
}

src_install() {
	rm -rvf "${S}"_build/lib/ncbi || die
	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"

#	dobin "${S}"_build/bin/*
#	dolib.so "${S}"_build/lib/*so*
#	dolib.a "${S}"_build/lib/*.a
#	doheader "${S}"_build/inc/*

	# File collisions with sci-biology/ncbi-tools
	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2

	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
	doenvd "${S}/99${PN}"
}

pkg_postinst() {
	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
}