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156 lines
4.5 KiB
156 lines
4.5 KiB
# Copyright 1999-2013 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.6 2013/06/12 11:31:50 jlec Exp $
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EAPI=5
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inherit eutils flag-o-matic prefix toolchain-funcs
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DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
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HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
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SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
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SLOT="0"
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LICENSE="public-domain"
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KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
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IUSE="doc static-libs X"
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RDEPEND="
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app-shells/tcsh
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dev-lang/perl
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media-libs/libpng
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X? ( x11-libs/motif:0 )"
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DEPEND="${RDEPEND}"
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S="${WORKDIR}/ncbi"
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EXTRA_VIB="asn2all asn2asn"
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pkg_setup() {
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echo
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ewarn 'Please note that the NCBI toolkit (and especially the X'
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ewarn 'applications) are known to have compilation and run-time'
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ewarn 'problems when compiled with agressive compilation flags. The'
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ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
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ewarn 'X support is enabled.'
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echo
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}
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src_prepare() {
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epatch \
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"${FILESDIR}"/${PN}-extra_vib.patch \
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"${FILESDIR}"/${P}-bfr-overflow.patch
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if use ppc || use ppc64; then
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epatch "${FILESDIR}"/${PN}-lop.patch
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fi
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if ! use X; then
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sed \
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-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
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-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
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-i "${S}"/make/makedis.csh || die
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else
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# X applications segfault on startup on x86 with -O3.
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use x86 || replace-flags '-O3' '-O2'
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fi
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# Apply user C flags...
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cd "${S}"/platform
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sed \
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-e "s:-O[s0-9]\?::g" \
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-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
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-e 's:-x[A-Z]*::g' \
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-e 's:-pipe::g' \
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-e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
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-e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
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-e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
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-e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
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-e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
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-e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
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-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
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-e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
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-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
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-i * || die
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# We use dynamic libraries
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sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
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sed \
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-re "s:/usr(/bin/.*sh):\1:g" \
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-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
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-i $(find "${S}" -type f) || die
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}
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src_compile() {
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export EXTRA_VIB
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cd "${WORKDIR}"
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csh ncbi/make/makedis.csh || die
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mkdir "${S}"/cgi "${S}"/real || die
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mv "${S}"/bin/*.cgi "${S}"/cgi || die
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mv "${S}"/bin/*.REAL "${S}"/real || die
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cd "${S}"/demo
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emake \
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-f ../make/makenet.unx \
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CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \
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LDFLAGS="${LDFLAGS}" \
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spidey
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cp spidey ../bin/ || die
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}
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src_install() {
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#sci-geosciences/cdat-lite
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mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
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dobin "${S}"/bin/*
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for i in ${EXTRA_VIB}; do
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dobin "${S}"/build/${i} || die "Failed to install binaries."
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done
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use static-libs && dolib.a "${S}"/lib/*.a
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mkdir -p "${ED}"/usr/include/ncbi
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cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
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die "Failed to install headers."
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# TODO: wwwblast with webapps
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#insinto /usr/share/ncbi/lib/cgi
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#doins ${S}/cgi/*
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#insinto /usr/share/ncbi/lib/real
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#doins ${S}/real/*
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# Basic documentation
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dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}}
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newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
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newdoc "${S}"/config/README README.config
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newdoc "${S}"/network/encrypt/README README.encrypt
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newdoc "${S}"/network/nsclilib/readme README.nsclilib
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newdoc "${S}"/sequin/README README.sequin
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mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
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doman "${S}"/doc/man/*
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# Hypertext user documentation
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dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
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insinto /usr/share/doc/${PF}/html
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doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
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# Developer documentation
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if use doc; then
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# Demo programs
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mkdir "${ED}"/usr/share/ncbi
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mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
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fi
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# Shared data (similarity matrices and such) and database directory.
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insinto /usr/share/ncbi
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doins -r "${S}"/data
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dodir /usr/share/ncbi/formatdb
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# Default config file to set the path for shared data.
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insinto /etc/ncbi
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newins "${FILESDIR}"/ncbirc .ncbirc
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eprefixify "${ED}"/etc/ncbi/.ncbirc
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# Env file to set the location of the config file and BLAST databases.
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newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
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}
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