my version

Signed-off-by: Justin Lecher <jlec@gentoo.org>

1 files changed, 345 insertions, 0 deletions

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
new file mode 100644
index 000000000..9806b413d
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -0,0 +1,345 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
+
+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 jpeg lzo 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 )
+	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
+
+# configure options, may want to expose some
+#  --without-debug         build non-debug versions of libs and apps
+#  --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-dll              build all libraries as DLLs
+#  --with-static           build all libraries statically even if --with-dll
+#  --with-static-exe       build all executables as statically as possible
+#  --with-plugin-auto-load always enable the plugin manager by default
+#  --with-bin-release      build executables suitable for public release
+#  --with-mt               compile in a MultiThread-safe manner
+#  --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-runpath=         hard-code the runtime path to DLLs
+#  --with-lfs              enable large file support to the extent possible
+#  --with-extra-action=    script to call after the configuration is complete
+#  --with-autodep          automatic generation of dependencies (GNU make)
+#  --with-build-root=DIR   specify a non-default build directory name
+#  --with-fake-root=DIR    appear to have been built under DIR
+#  --without-suffix        no Release/Debug, MT or DLL sfx in the build dir name
+#  --with-hostspec         add full host specs to the build dir name
+#  --without-version       don't always include the cplr ver in the bd name
+#  --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-bincopy          populate lib and bin with copies, not hard links
+#  --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            run test suite after the build
+#  --with-check-tools=...  use the specified tools for testing
+#  --with-ncbi-public      ensure compatibility for all in-house platforms
+#  --with-strip            strip binaries at build time
+#  --with-pch              use precompiled headers if possible
+#  --with-caution          cancel configuration unconditionally when in doubt
+#  --without-caution       proceed without asking when in doubt
+#  --without-ccache        do not automatically use ccache if available
+#  --without-distcc        do not automatically use distcc if available
+#  --without-ncbi-c        do not use NCBI C Toolkit
+#  --without-sss           do not use NCBI SSS libraries
+#  --without-utils         do not use NCBI SSS UTIL library
+#  --without-sssdb         do not use NCBI SSS DB library
+#  --with-included-sss     use the in-tree copy of SSS
+
+#  --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-ctools        do not build NCBI C Toolkit based projects
+#  --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
+
+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}"
+	tc-export CXX CC
+}
+
+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-utils
+	--with-sssdb
+	--with-included-sss
+	--with-z="${EPREFIX}"/usr
+	--with-bz2="${EPREFIX}"/usr
+	--with-muparser="${EPREFIX}"/usr
+	--without-sybase
+#	--with-3psw=std:netopt
+	$(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-m)
+	$(use_with wxwidgets wxwidgets "${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)
+	$(use_with xml libxml2 "${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)
+	)
+
+	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
+	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+	# TODO
+    # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
+
+	"${S}"/configure \
+	--prefix="${EPREFIX}"/usr \
+	--build=x86_64-pc-linux-gnu \
+	--host=x86_64-pc-linux-gnu \
+	--infodir=/usr/share/info \
+	--datadir=/usr/share \
+	--sysconfdir=/etc \
+	--localstatedir=/var/lib \
+	--libdir=/usr/lib64 \
+	${myconf[@]} || die
+#--without-debug \
+#		--with-bin-release \
+#		--with-bincopy \
+#		--without-static \
+#		--with-dll \
+#		--with-mt \
+#		--with-lfs \
+#		--prefix="${ED}"/usr \
+#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
+#		|| die
+#	econf ${myconf[@]}
+}
+
+src_compile() {
+	# all_r would ignore the --with-projects contents and build more
+	# emake all_r -C GCC*-Release*/build || die
+	# all_p with compile only selected/required components
+	emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+}
+
+src_install() {
+	emake install || die
+	# File collisions with sci-biology/ncbi-tools
+	rm -f "${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/'
+}