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# Copyright 1999-2007 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.14 2007/10/13 23:09:17 je_fro Exp $
inherit flag-o-matic toolchain-funcs eutils
DESCRIPTION="Development toolkit and applications (BLAST, entrez, ddv, udv, sequin...) 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 )"
SLOT="0"
KEYWORDS="alpha amd64 ppc ppc64 sparc x86"
IUSE="doc X"
DEPEND="app-shells/tcsh
dev-lang/perl
media-libs/libpng
X? ( virtual/motif )"
S="${WORKDIR}/ncbi"
pkg_setup() {
echo
ewarn 'It is important to note that the NCBI tools (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. If you experience difficulties with this'
ewarn 'package and use agressive "CFLAGS", lower the "CFLAGS" and try'
ewarn 'to install the NCBI tools again.'
echo
}
src_unpack() {
unpack ${A}
use ppc64 && cd "${S}" && epatch "${FILESDIR}/${PN}-lop.patch"
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 = $(tc-getCC)/" linux.ncbi.mk || die
}
src_compile() {
cd "${WORKDIR}"
ncbi/make/makedis.csh || die
mkdir "${S}/cgi"
mkdir "${S}/real"
mv "${S}/bin/*.cgi" "${S}/cgi"
mv "${S}/bin/*.REAL" "${S}/real"
}
src_install() {
dobin "${S}/bin/*"
dolib "${S}/lib/*"
mkdir -p "${D}/usr/include/ncbi"
cp -RL "${S}/include/*" "${D}/usr/include/ncbi"
# 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}}"
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 "${S}/sequin/README README.sequin"
doman "${S}/doc/man/*"
# Hypertext user documentation
dohtml "${S}/{README.html,doc/{*.html *.gif}}"
insinto /usr/share/doc/${PF}/html/blast
doins "${S}/doc/blast/*"
# Developer documentation
if use doc; then
# "socks" documentation
SOCKS="network/socks/socks.cstc.4.2"
insinto /usr/share/doc/${PF}/socks
doins "${S}/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects}"
newins "${S}/${SOCKS}/libident/README README.libident"
doins "${S}/${SOCKS}/sockd/sockd.conf.sample"
doman "${S}/${SOCKS}/{doc/*.{1,5,8},libident/ident.3}"
# "regexp" documentation
insinto /usr/share/doc/${PF}/regexp
doins "${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}"
insinto /usr/share/doc/${PF}/regexp/html
doins "${S}/regexp/doc/*.html"
doman "${S}/regexp/doc/*.{1,3}"
# Hypertext SDK documentation
insinto /usr/share/doc/${PF}/html/sdk
doins "${WORKDIR}/${PN}-sdk-doc/*"
# Demo programs
mkdir "${D}/usr/share/ncbi"
mv "${S}/demo ${D}/usr/share/ncbi/demo"
mv "${S}/regexp/demo" "${D}/usr/share/ncbi/demo/regexp"
mv "${S}/regexp/test" "${D}/usr/share/ncbi/demo/regexp/test"
fi
# Shared data (similarity matrices and such) and database directory.
insinto /usr/share/ncbi/data
doins "${S}/data/*"
dodir /usr/share/ncbi/formatdb
# Default config file to set the path for shared data.
insinto /etc/ncbi
newins "${FILESDIR}/ncbirc" .ncbirc
# Env file to set the location of the config file and BLAST databases.
newenvd "${FILESDIR}/21ncbi-r1" 21ncbi
}
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