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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit eutils 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 -> ${P}.tar.gz"
SLOT="0"
LICENSE="public-domain"
KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE="doc static-libs X"
RDEPEND="
app-shells/tcsh
dev-lang/perl
media-libs/libpng:0=
X? (
media-libs/fontconfig
x11-libs/motif:0=
x11-libs/libICE
x11-libs/libX11
x11-libs/libXft
x11-libs/libXmu
x11-libs/libXt
)"
DEPEND="${RDEPEND}"
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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