--- /dev/null
+# Copyright 1999-2005 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-r1.ebuild,v 1.1 2005/11/15 00:29:53 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="~amd64 ~ppc ~ppc-macos ~ppc64 ~x86"
+IUSE="doc mpi X"
+
+DEPEND="app-shells/tcsh
+ dev-lang/perl
+ media-libs/libpng
+ mpi? ( virtual/mpi )
+ X? ( virtual/x11
+ 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 "${FILESDIR}"/${P}-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
+ mv "${S}"/bin/*.REAL "${S}"/real
+
+ 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 "${S}"/bin/*
+ dolib "${S}"/lib/*
+ mkdir -p "${D}"/usr/include/ncbi
+ cp -RL "${S}"/include/* "${D}"/usr/include/ncbi
+
+ if use mpi; then
+ cd "${WORKDIR}"/mpiblast-1.4.0
+ make install DESTDIR="${D}" || die
+ 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}}
+ 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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