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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit toolchain-funcs
MY_PV=${PV//./}
DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"
SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
S="${WORKDIR}/${PN}3.02"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
app-shells/tcsh
sci-biology/elph"
PATCHES=(
"${FILESDIR}"/${P}-jobserver-fix.patch
"${FILESDIR}"/${P}-ldflags.patch
"${FILESDIR}"/${P}-rename_extract.patch
)
src_prepare() {
sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
# Fix Makefile to die on failure
sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
# GCC 4.3 include fix
sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die
#
sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die
sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die
sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die
sed -i "s/@ if/if/" src/c_make.gen || die
# avoid file collision on /usr/bin/extract #247394
default
}
src_compile() {
emake \
-C src \
CC="$(tc-getCC)" \
CXX="$(tc-getCXX)" \
AR="$(tc-getAR)" \
CXXFLAGS="${CXXFLAGS}" \
CFLAGS="${CFLAGS}" \
LDFLAGS="${LDFLAGS}"
}
src_install() {
rm bin/test || die
dobin bin/*
insinto /usr/share/glimmer
doins -r scripts
dodoc glim302notes.pdf
}
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