# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

DESCRIPTION="Consed: a genome sequence finishing X11 program (editor, autofinish, autoreport,
autoedit, and align reads to reference sequence)"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"

# FIXME: change the SRC_URI based on the ARCH
# available files:
# consed_linux32bit.tar.Z
# consed_linux64bit.tar.Z
# consed_linux_itanium.tar.Z
SRC_URI="consed_linux32bit.tar.Z"

# this is the sourcecode of consed apllication but no other tools are here
# SRC_URI="sources.tar.Z"

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

DEPEND=""
RDEPEND="dev-lang/perl
		>=sci-biology/phrap-1.080721
		>=sci-biology/phd2fasta-0.990622"

S="${WORKDIR}"

RESTRICT="fetch"

pkg_nofetch() {
	einfo "Please visit http://bozeman.mbt.washington.edu/consed/consed.html and obtain the file"
	# einfo '"sources.tar.Z",  and put it in'
	einfo "consed_linux32bit.tar.Z or consed_linux64bit.tar.Z or"
	einfo "consed_linux_itanium.tar.Z and optionally also sources.tar.Z put it in ${DISTDIR}"
	einfo "The sources.tar.Z is at the moment not utilized by this ebuild as"
	einfo "they lack some header file new.h"
	einfo
	einfo "In addition, you may download from your registered IP address also fixes from"
	einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/phredPhrap"
	einfo "and additional tools from"
	einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/filter454Reads.perl"
	einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/add454Reads.perl"
	einfo "and the ebuild will place them into scripts/"

	einfo "There will be two consed* binaries installed. One statically linked"
	einfo "and one dynamically linked against libstdc++-libc6.2-2.so.3 from"
	einfo "authors. Finally, a soflink to the static binary will be created"
	einfo "in your installation layout as /usr/bin/consed"
}

src_compile() {
	cd scripts
	# zap the following three lines from the perl file phredPhrap and insert one
	# pointing to a Gentoo place in /usr/share/phred/phredpar.dat
	#$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
	##$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
	##$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
	ln -s phredPhrap polyphredPhrap

	pwd
	cd ..

	#FIXME: cannot compile anyway because new.h is missing
	einfo "Please test whether -DX86_GCC_LINUX works also on amd64 platforms, probably yes"
	einfo "but how about other targets?"

	#FIXME: propagate $CFLAGS into the Makefile
	# sed -i 's/#LXFLAGS= -DX86_GCC_LINUX/LXFLAGS= -DX86_GCC_LINUX/' Makefile
	# make -f makefile_linux32bit || die "make -f makefile_linux32bit failed"

	# compile additional utilites
	cd misc

	# co not overwrite /usr/bin/phd2fasta as user should install the updated
	# version distributed always separately sci-biology/phd2fasta-20080822
	# cd phd2fasta
	# make
	# cd ..

	cd mktrace/
	make
	cd ..

	cd 454/
	gcc sff2phdball.c -o sff2phdball
	gcc sff2scf.c -o sff2scf
	cd ../
}

src_install() {
	ln -s consed_linux32bit consed
	newenvd "${FILESDIR}"/consed 21consed|| die "Failed to install env file."

	dobin consed consed_linux32bit consed_linux32bit_dyn misc/454/sff2phdball misc/454/sff2scf misc/mktrace/mktrace scripts/phredPhrap scripts/polyphredPhrap scripts/*.perl contributions/*.perl
	for i in {README,17.0_announcement}.txt ; do
		dodoc ${i}
	done
	dodir /usr/share/consed-bin/examples
	insinto /usr/share/consed-bin/examples
	doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions	selectRegionsAnswer
}