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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit fortran-2 perl-module toolchain-funcs
DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
HOMEPAGE="https://sourceforge.net/projects/estscan/"
SRC_URI="
https://downloads.sourceforge.net/${PN}/${P}.tar.gz
https://downloads.sourceforge.net/${PN}/At.smat.gz
https://downloads.sourceforge.net/${PN}/Dm.smat.gz
https://downloads.sourceforge.net/${PN}/Dr.smat.gz
https://downloads.sourceforge.net/${PN}/Hs.smat.gz
https://downloads.sourceforge.net/${PN}/Mm.smat.gz
https://downloads.sourceforge.net/${PN}/Rn.smat.gz
https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"
SLOT="0"
LICENSE="estscan"
KEYWORDS="~amd64 ~x86"
IUSE="icc ifc"
DEPEND="
dev-perl/BTLib
icc? ( dev-lang/icc )
ifc? ( dev-lang/ifc )"
RDEPEND="${DEPEND}"
S="${WORKDIR}"
src_prepare() {
default
sed \
-e 's/\\rm -f/rm -rf/' \
-e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
-i "${P}"/Makefile || die "failed to edit Makefile"
# fix hard-coded paths
sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die
sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die
if ! use icc; then
sed \
-e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die
fi
if ! use ifc; then
sed \
-e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
-e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \
|| die
fi
if use icc; then
# FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives
# me gcc instead, same for $(tc-getF77)
# Moreover, the if/else logic here should separate users having only icc
# while not ifort (and vice-versa) from those having only
# gcc/gfortran/g77
#
# FIXME: below as a dirty hack I force gfortran instead of ifort for
# my testing purposes. Didn't ebuild contain "PROVIDES" line?
# Same for FFLAGS.
sed \
-e "s:^# CC = icc:CC = icc:" \
-e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \
-e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
-e "s/^ CC = gcc/# CC = gcc/" \
-i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC"
fi
if use ifc; then
sed \
-e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \
-e "s/^# F77 = ifort/F77 = gfortran/" \
-e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
-e "s/^ F77 = g77/# F77 = g77/" \
-i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77"
fi
}
src_compile() {
emake -C ${P}
}
src_install() {
# FIXME: Some kind of documentation is in {P}/${PN}.spec
cd ${P} || die "Failed to chdir to ${P}"
dobin \
build_model ${PN} evaluate_model extract_EST extract_UG_EST \
extract_mRNA makesmat maskred prepare_data winsegshuffle
# the file build_model_utils.pl should go into some PERL site-packages dir
# see {P}/${PN}.spec
# install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension
insinto /usr/share/doc/${PN}
# grab the file directly from ../distdir/
doins "${DISTDIR}"/user_guide_fev_07.pdf
# install the default precomputed matrices
cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}"
insinto /usr/share/${PN}
doins *.smat
# install BTlib (in perl)
# dobin fetch indexer netfetch
insinto /usr/share/${PN}/
# install the config file which is packed inside the BTLib tarball while is not
# being installed by dev-perl/BTLib
doins "${WORKDIR}"/BTLib-0.19/fetch.conf
# FIXME: install the *.pm files from BTLib-0.19
# cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19
# myinst="DESTDIR=${D}"
# perl-module_src_install
einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout."
einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/."
einfo "You may follow the hints from http://${PN}.sourceforge.net/"
}
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