| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| inherit eutils flag-o-matic prefix toolchain-funcs |
| |
| DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST" |
| HOMEPAGE="http://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/${i} || die "Failed to install binaries." |
| done |
| use static-libs && dolib.a "${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 |
| } |