# 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 1.3 2006/02/02 02:51:41 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}"/${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 "${S}"/cgi || die
	mv "${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."
}