From 3b08f674e3f771b49370edb144dab0958c8cf721 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Tue, 31 Aug 2021 08:59:54 +0100
Subject: gentoo resync : 31.08.2021

---
 sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 ---------------------
 1 file changed, 169 deletions(-)
 delete mode 100644 sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild

(limited to 'sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild')

diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild
deleted file mode 100644
index cec2f688b661..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild
+++ /dev/null
@@ -1,169 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch flag-o-matic prefix toolchain-funcs
-
-DESCRIPTION="Development toolkit and applications for computational biology, including BLAST"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc static-libs X"
-
-RDEPEND="
-	app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng:0=
-	virtual/glu
-	virtual/opengl
-	X? (
-		media-libs/fontconfig
-		x11-libs/motif:0=
-		x11-libs/libICE
-		x11-libs/libX11
-		x11-libs/libXft
-		x11-libs/libXmu
-		x11-libs/libXt
-		)"
-DEPEND="
-	${RDEPEND}
-	virtual/pkgconfig
-"
-
-S="${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_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-extra_vib.patch \
-		"${FILESDIR}"/${P}-bfr-overflow.patch \
-		"${FILESDIR}"/${P}-format-security.patch \
-		"${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch
-
-	if use ppc || use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if ! use X; then
-		sed \
-			-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i "${S}"/make/makedis.csh || die
-	else
-		# X applications segfault on startup on x86 with -O3.
-		use x86 || replace-flags '-O3' '-O2'
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	sed \
-		-e "s:-O[s0-9]\?::g" \
-		-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
-		-e 's:-x[A-Z]*::g' \
-		-e 's:-pipe::g' \
-		-e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
-		-e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
-		-e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
-		-e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
-		-e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
-		-e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
-		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
-		-e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-		-i * || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	sed \
-		-re "s:/usr(/bin/.*sh):\1:g" \
-		-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
-		-i $(find "${S}" -type f) || die
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	csh ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi "${S}"/real || die
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-	cd "${S}"/demo
-	emake \
-		-f ../make/makenet.unx \
-		CC="$(tc-getCC) ${CFLAGS} -I../include  -L../lib" \
-		LDFLAGS="${LDFLAGS}" \
-		spidey
-	cp spidey ../bin/ || die
-}
-
-src_install() {
-	#sci-geosciences/cdat-lite
-	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
-
-	dobin "${S}"/bin/*
-
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i}
-	done
-	use static-libs && dolib.a "${S}"/lib/*.a
-	mkdir -p "${ED}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${ED}"/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.*}}
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
-	newdoc "${S}"/config/README README.config
-	newdoc "${S}"/network/encrypt/README README.encrypt
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib
-	newdoc "${S}"/sequin/README README.sequin
-	mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
-	doman "${S}"/doc/man/*
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
-	insinto /usr/share/doc/${PF}/html
-	doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
-
-	# Developer documentation
-	if use doc; then
-		# Demo programs
-		mkdir "${ED}"/usr/share/ncbi
-		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi
-	doins -r "${S}"/data
-	dodir /usr/share/ncbi/formatdb
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc
-	eprefixify "${ED}"/etc/ncbi/.ncbirc
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
-}
-- 
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