# 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
}