# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

inherit toolchain-funcs

DESCRIPTION="Consed: a genome sequence finishing program"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
SRC_URI="consed-19-sources.tar.gz
	consed-19-linux.tar.gz"

LICENSE="phrap"
SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""

DEPEND="x11-libs/openmotif"
RDEPEND="${DEPEND}
	>=sci-biology/phrap-1.080721"

S="${WORKDIR}"

RESTRICT="fetch"

pkg_nofetch() {
	einfo "Please visit ${HOMEPAGE} and obtain the file"
	einfo "\"sources.tar.gz\", then rename it to \"consed-${PV}-sources.tar.gz\""
	einfo "and place it in ${DISTDIR},"
	einfo "obtain the file"
	einfo "\"consed_linux.tar.gz\", then rename it to \"consed-${PV}-linux.tar.gz\""
	einfo "and place it in ${DISTDIR}"
}

src_unpack() {
	unpack ${A}
	# todo: cflags
	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
	sed -i '/lib/ s/X11R6//g' "${S}/makefile" || die
}

src_compile() {
	emake || die
	emake -C misc/mktrace || die
	emake -C misc/phd2fasta || die
	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
}

src_install() {
	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
	dobin scripts/* || die
	insinto /usr/share/${PN}/examples
	doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions selectRegionsAnswer || die
	dodoc README.txt *_announcement.txt
}