Cleaned old version

(Portage version: 2.2_rc67/cvs/Linux x86_64)

5 files changed, 6 insertions, 805 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 1422ceffe33f..65f815c36cf6 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.77 2010/03/29 09:45:07 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.78 2010/06/24 20:41:40 jlec Exp $
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> -ncbi-tools-20060507.ebuild,
+  -ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild,
+  -ncbi-tools-20090301.ebuild:
+  Cleaned old version
 
   29 Mar 2010; Pacho Ramos <pacho@gentoo.org> ncbi-tools-20090809.ebuild:
   amd64 stable, bug 298779
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild
deleted file mode 100644
index b5ef652bfe2d..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild
+++ /dev/null
@@ -1,197 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild,v 1.12 2008/06/27 10:23:37 ulm Exp $
-
-inherit flag-o-matic toolchain-funcs eutils autotools
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )
-	mpi? ( mirror://gentoo/mpiblast-20060625.tar.gz )"
-
-SLOT="0"
-KEYWORDS="alpha amd64 ppc ppc64 sparc x86"
-IUSE="doc mpi X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	mpi? ( virtual/mpi )
-	X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
-	sys-devel/pmake"
-
-S="${WORKDIR}/ncbi"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-asn2all.patch
-
-	if use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if use mpi; then
-		cd "${WORKDIR}"
-		epatch "${WORKDIR}"/mpiblast/ncbi_Dec2005_evalue.patch
-	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
-	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
-	cd "${S}"/make
-	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
-			"Failed to replace make by pmake."
-}
-
-src_compile() {
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		AM_OPT="-a"
-		eautoreconf
-		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
-		emake || die
-	fi
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	dobin "${S}"/build/asn2all || die "Failed to install binaries."
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		make install DESTDIR="${D}" || die "Failed to install MPI blast."
-	fi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
-
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild
deleted file mode 100644
index 9ca781f6b1a8..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild
+++ /dev/null
@@ -1,202 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild,v 1.3 2008/06/27 10:23:37 ulm Exp $
-
-inherit flag-o-matic toolchain-funcs eutils autotools
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )
-	mpi? ( mirror://gentoo/mpiblast-20060625.tar.gz )"
-
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
-IUSE="doc mpi X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	mpi? ( virtual/mpi )
-	X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
-	sys-devel/pmake"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
-
-	if use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if use mpi; then
-		cd "${WORKDIR}"
-		epatch "${WORKDIR}"/mpiblast/ncbi_Dec2005_evalue.patch
-	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
-	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
-	cd "${S}"/make
-	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
-			"Failed to replace make by pmake."
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		AM_OPT="-a"
-		eautoreconf
-		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
-		emake || die
-	fi
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
-	done
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		make install DESTDIR="${D}" || die "Failed to install MPI blast."
-	fi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
-
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
deleted file mode 100644
index d7b6e6bc34b6..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild,v 1.7 2008/06/27 10:23:37 ulm Exp $
-
-inherit flag-o-matic toolchain-funcs eutils autotools
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )"
-
-#	mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )
-
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
-
-# IUSE="doc mpi X"
-# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release.
-# Currently seeking a fix.
-
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
-	sys-devel/pmake"
-
-#	mpi? ( virtual/mpi )
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
-
-	if use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-#	if use mpi; then
-#		cd "${WORKDIR}"
-#		epatch "${WORKDIR}"/mpiblast/ncbi_Mar2007_evalue.patch
-#	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic 64-bit Linux...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic 64-bit Linux...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
-	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
-	cd "${S}"/make
-	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
-			"Failed to replace make by pmake."
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-
-# mpiblast fails to compile... perhaps mpiblast2 contain a fix
-#	if use mpi; then
-#		cd "${WORKDIR}"/mpiblast
-#		AM_OPT="-a"
-#		eautoreconf
-#		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
-#		emake || die
-#	fi
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
-	done
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-#	if use mpi; then
-#		cd "${WORKDIR}"/mpiblast
-#		make install DESTDIR="${D}" || die "Failed to install MPI blast."
-#	fi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
-
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild
deleted file mode 100644
index 362063bc4f0c..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild
+++ /dev/null
@@ -1,185 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild,v 1.5 2009/09/22 14:29:57 maekke Exp $
-
-EAPI="1"
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-
-#SRC_URI="mirror://gentoo/${P}.tar.gz"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz"
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 x86"
-
-# IUSE=mpi deprecated, use sci-biology/mpiblast separately
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
-
-	if use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic 64-bit Linux...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic 64-bit Linux...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
-	done
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	# TODO: wwwblast with webapps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}