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# Copyright 1999-2006 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-r2.ebuild,v 1.4 2006/06/27 01:44:20 ribosome 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 )
mpi? ( mirror://gentoo/mpiBLAST-1.4.0.tgz )"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc ~ppc-macos ~ppc64 ~sparc ~x86"
IUSE="doc mpi X"
DEPEND="app-shells/tcsh
dev-lang/perl
media-libs/libpng
mpi? ( virtual/mpi )
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 ${A}
if use ppc64; then
cd "${S}"
epatch "${FILESDIR}"/${PN}-lop.patch
fi
if use mpi; then
cd "${S}"
epatch "${WORKDIR}"/mpiblast-1.4.0/ncbi_Jun2005_evalue.patch
fi
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 || die
mv "${S}"/bin/*.REAL "${S}"/real || die
if use mpi; then
cd "${WORKDIR}"/mpiblast-1.4.0
econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
emake || die
fi
}
src_install() {
dobin "${S}"/bin/* || die "Failed to install binaries."
dolib "${S}"/lib/* || die "Failed to install libraries."
mkdir -p "${D}"/usr/include/ncbi
cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
die "Failed to install headers."
if use mpi; then
cd "${WORKDIR}"/mpiblast-1.4.0
make install DESTDIR="${D}" || die "Failed to install MPI blast."
fi
# 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}} || \
die "Failed to install basic documentation."
newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
die "Failed renaming fa2htgs documentation."
newdoc "${S}"/config/README README.config || \
die "Failed renaming config documentation."
newdoc "${S}"/network/encrypt/README README.encrypt || \
die "Failed renaming encrypt documentation."
newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
die "Failed renaming nsclilib documentation."
newdoc "${S}"/sequin/README README.sequin || \
die "Failed renaming sequin documentation."
doman "${S}"/doc/man/* || \
die "Failed to install man pages."
# Hypertext user documentation
dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
die "Failed to install HTML documentation."
insinto /usr/share/doc/${PF}/html/blast
doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
# Developer documentation
if use doc; then
# "socks" documentation
SOCKS="network/socks/socks.cstc.4.2"
insinto /usr/share/doc/${PF}/socks
doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} || die
newins "${S}"/${SOCKS}/libident/README README.libident
doins "${S}"/${SOCKS}/sockd/sockd.conf.sample || die
doman "${S}"/${SOCKS}/{doc/*.{1,5,8},libident/ident.3} || die
# "regexp" documentation (No longer installed, see bug #115463.)
# 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/* || die
# Demo programs
mkdir "${D}"/usr/share/ncbi
mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
mv "${S}"/regexp/demo "${D}"/usr/share/ncbi/demo/regexp || die
mv "${S}"/regexp/test "${D}"/usr/share/ncbi/demo/regexp/test || die
fi
# Shared data (similarity matrices and such) and database directory.
insinto /usr/share/ncbi/data
doins "${S}"/data/* || die "Failed to install shared data."
dodir /usr/share/ncbi/formatdb || die
# Default config file to set the path for shared data.
insinto /etc/ncbi
newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
# Env file to set the location of the config file and BLAST databases.
newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
}
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