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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline"
HOMEPAGE="http://mblab.wustl.edu/software/twinscan"
SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz"
LICENSE="all-rights-reserved"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
DEPEND="dev-libs/glib:2"
RDEPEND="${DEPEND}"
S="${WORKDIR}/N-SCAN"
src_prepare() {
sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl || die
sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die
tc-export CC AR RANLIB
sed \
-e 's:ar :$(AR) :g' \
-e 's:ranlib :$(RANLIB) :g' \
-e 's: -o : $(LDFLAGS) -o :g' \
-i Makefile || die
sed \
-e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \
-e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \
-i Makefile.include || die
}
src_install() {
# TODO: prevent file collision with media-gfx/iscan by renaming iscan to iscan_twinscan
# also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
rm bin/test.pl || die
dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
dolib lib/libzoe.a
insinto /usr/share/${PN}
doins -r parameters
insinto /usr/share/${PN}/src
doins src/*.zhmm
perl_set_version
insinto ${VENDOR_LIB}/${PN}
doins lib/perl5/*.pm
echo "TWINSCAN=/usr" > "${S}"/99${PN}
doenvd "${S}"/99${PN}
rm -rf examples/tmp
dodoc examples/* README* src/doc/*.txt
}
pkg_postinst(){
einfo "Pairagon acts on output from either: sci-biology/gmap sci-biology/blat."
einfo "It also works on blastn output from WU-BLAST (not provided in Gentoo)."
einfo "It also calls blastz (seems superseded by LASTZ) and genscan++ (not provided in Gentoo)."
einfo "For some reason we have pslCDnaFilter provided only by sci-biology/ucsc-genome-browser"
}
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