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

DESCRIPTION="The TIGR Gene Indices Clustering Tools (TGICL) for genomic data processing: tgicl, seqclean, cln2qual, mdust, trimpoly, zmsort, tclust, sclust, cdbfasta, psx"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"

for i in seqclean/{mdust,seqclean,seqcl_scripts,trimpoly} cdbfasta/cdbfasta \
	tgicl/{mgblast,nrcl,psx,pvmsx,sclust,tclust,tgi_cpp_library,tgicl_linux,tgicl_scripts,zmsort} \
	clview/clview_src clview/clview_linux_i386; do
	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz"
done

LICENSE="Artistic"
SLOT="0"
IUSE="pvm"
KEYWORDS="~x86"

DEPEND="pvm? ( sys-cluster/pvm )
	x11-libs/fox"

# mgblast needs old version of ncbi-tools unpacked and compiled during its own compilation
# from newer tools you need to include blfmtutl.h but the next errir is no go:
#   mgblast.c:2205: error: too few arguments to function ‘BXMLBuildOneQueryIteration’
RDEPEND="${DEPEND}
	sci-biology/ncbi-tools
	sci-biology/cap3-bin
	dev-lang/perl"

S=${WORKDIR}

src_unpack() {
	unpack {nrcl,sclust,tclust,zmsort,mdust,seqclean,seqcl_scripts,trimpoly,cdbfasta,mgblast,tgi_cpp_library,tgicl_linux,tgicl_scripts,clview_src}.tar.gz
	for i in psx pvmsx; do
		mkdir "${S}"/${i}
		cd "${S}/${i}"
		unpack ${i}.tar.gz
		cd ..
	done
	cd clview
	unpack clview_linux_i386.tar.gz
	cd ..
	mv mgblast/makefile mgblast/Makefile
}

src_compile() {
	einfo "You might download UniVec from NCBI if you do not have your own"
	einfo "fasta file with vector sequences you want to remove from sequencing"
	einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"

	# disable the necessity to install Mailer.pm with this tool
	einfo "Disabling mailer feature withing seqclean"
	sed -i 's/use Mailer;/#use Mailer;/' seqclean/seqclean

	######################################################################
	# clview with tgi_cl/gcl stuff cannot be compiled
	#
	# FIXME: we have to run `/usr/bin/fox-config --cflags' to yield
	#        `-I/usr/include/fox-1.6'
	# similarly `fox-config --libs' to yield e.g.
	# `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11
	# -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm
	# -lcups -lnsl -lGLU -lGL'
	FOXINCPATH='-I/usr/include/fox-1.6'
	FOXLIBS='-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11 -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz	-lbz2 -lm -lcups -lnsl -lGLU -lGL'
	
	sed -i "s/FOXDIR := \/tucan\/src\/fox-1.0.3/#FOXDIR := \/tucan\/src\/fox-1.0.3/" clview/Makefile || die "a"
	sed -i 's#-I${FOXDIR}/include#-I/usr/include/fox-1.6#' clview/Makefile || die "d"
	sed -i "s#-L${FOXDIR}/src/.libs##" clview/Makefile || die "here"
	sed -i "s#LOADLIBES := -lm -lXext -lFOX#LOADLIBES := -lFOX-1.6 -lXext -lX11	-lXft -lXrender -lfontconfig -lfreetype -lz -lX11 -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz    -lbz2 -lm -lcups -lnsl -lGLU -lGL#" clview/Makefile || die "v"
	sed -i "s#-I-#-iquote#" clview/Makefile

	# see tgi_cl/gcl/
	sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../tgi_cl#" clview/Makefile || die
	cd ${S}/clview
	# is used in conjunction with clview_src.tar.gz
	make
	cd ..
	######################################################################



	# mgblast cannot be compiled against newer ncbi-tools but let's try
	sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' mgblast/Makefile
	sed -i 's#NCBI_INCDIR = $(NCBI_TOOLKIT)/include#NCBI_INCDIR = $(NCBI_TOOLKIT)/include/ncbi#' mgblast/Makefile
	sed -i "s#-I-#-iquote#" mgblast/Makefile
	cd ${S}/mgblast
	make || cp ../tgicl_linux/bin/mgblast .
	cd ..

	sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' zmsort/zmsort.cpp

	# the PVM-related binaries are compiled only when PVM is installed but
	# anyway, the binaries are available in tgicl_linux/bin/ just in case
	for i in nrcl cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
		sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
			${S}/${i}/Makefile
		sed -i "s#-I-#-iquote#" ${S}/${i}/Makefile
		cd "${S}/${i}" || die "cd ${i} failed"
		emake || die "emake failed in ${i}"
	done
}

src_install() {
	dobin cdbfasta/{cdbfasta,cdbyank}
	dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx}
	dobin tgicl_scripts/tgicl tgicl_scripts/bin/tgicl_asm.psx tgicl_scripts/bin/tgicl_cluster.psx
	
	# an old version of cap3 is available but we REQUIRE sci-biology/cap3-bin
	# newbin tgicl_linux/bin/cap3 /usr/bin/cap3.old

	for i in mgblast mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
		dobin ${i}/${i}
	done
	for i in cdbfasta seqclean tgicl_linux mgblast trimpoly tgicl_scripts; do
		newdoc ${i}/README README.${i}
	done

	# install at least the binaries for clview when we cannot compile it
	dobin clview/clview
	dolib clview/libFOX-1.0.so.0
	dolib clview/libFOX-1.0.so.0.0.3
}