| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI="5" |
| |
| inherit eutils toolchain-funcs |
| |
| MY_PV=${PV//./} |
| |
| DESCRIPTION="An HMM-based microbial gene finding system from TIGR" |
| HOMEPAGE="http://ccb.jhu.edu/software/glimmer" |
| SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz" |
| |
| LICENSE="Artistic" |
| SLOT="0" |
| IUSE="" |
| KEYWORDS="~amd64 ~x86" |
| |
| DEPEND="" |
| RDEPEND="app-shells/tcsh |
| sci-biology/elph" |
| |
| #S="${WORKDIR}/${PN}${PV}" |
| S="${WORKDIR}/${PN}3.02" |
| |
| PATCHES=( |
| "${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) $(TGT) || exit 1/' src/c_make.gen || die |
| # GCC 4.3 include fix |
| sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die |
| # |
| sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die |
| sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die |
| sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die |
| sed -i "s/@ if/if/" src/c_make.gen || die |
| # avoid file collision on /usr/bin/extract #247394 |
| epatch "${PATCHES[@]}" |
| } |
| |
| src_compile() { |
| emake \ |
| -C src \ |
| CC=$(tc-getCC) \ |
| CXX=$(tc-getCXX) \ |
| AR=$(tc-getAR) \ |
| CXXFLAGS="${CXXFLAGS}" \ |
| CFLAGS="${CFLAGS}" \ |
| LDFLAGS="${LDFLAGS}" |
| } |
| |
| src_install() { |
| rm bin/test || die |
| dobin bin/* |
| |
| insinto /usr/share/${PN} |
| doins -r scripts |
| |
| dodoc glim302notes.pdf |
| } |