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