Diff hmmer-2.3.2-r4 with a hmmer-3.1_beta2

/usr/portage/sci-biology/hmmer/hmmer-3.1_beta2.ebuild 2017-02-28 22:50:00.000000000 +0300
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# Copyright 1999-2017 Gentoo Foundation
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# Copyright 1999-2016 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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MY_PV="${PV/_beta/b}"
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DESCRIPTION="Sequence analysis using profile hidden Markov models"
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LICENSE="GPL-2"
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HOMEPAGE="http://hmmer.org/"
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SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
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SLOT="2"
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IUSE="altivec test threads"
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KEYWORDS="~amd64 ~x86"
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SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
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DEPEND="test? ( dev-lang/perl )"
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RDEPEND=""
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LICENSE="GPL-3"
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SLOT="0"
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IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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RDEPEND="
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	mpi? ( virtual/mpi )
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	gsl? ( sci-libs/gsl:= )"
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DEPEND="${RDEPEND}
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	test? ( dev-lang/perl )"
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S="${WORKDIR}/${PN}-${MY_PV}"
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PATCHES=(
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	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
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	"${FILESDIR}/${P}-fix-build-system-destdir.patch"
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	"${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
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	"${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
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)
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src_configure() {
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	# prevent stray environmental variable
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	# from causing issues in the test phase
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	unset TMPDIR
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	# make build verbose, bug 429308
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	export V=1
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	econf \
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		--enable-lfs \
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		$(use_enable altivec) \
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		$(use_enable threads)
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		--disable-pic \
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		$(use_enable altivec vmx) \
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		$(use_enable cpu_flags_x86_sse sse) \
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		$(use_enable mpi) \
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		$(use_enable threads) \
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		$(use_with gsl)
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}
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src_install() {
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	default
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	dodoc Userguide.pdf
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	newlib.a src/libhmmer.a libhmmer2.a
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	insinto /usr/include/hmmer2
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	doins src/*.h
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	dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
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	dolib.a squid/libsquid.a
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	insinto /usr/include/hmmer2
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	doins squid/*.h
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	dodoc NOTES Userguide.pdf
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	newdoc 00README README
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	# rename files due to collisions with hmmer-3
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	# in order to make SLOTing possible
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	local i
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	# first rename man pages...
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	pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die
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	for i in hmm*.1; do
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		mv ${i%.1}{,2}.1 || die
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	done
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	popd >/dev/null || die
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	# ... then rename binaries
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	pushd "${ED%/}"/usr/bin/ >/dev/null || die
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	for i in hmm*; do
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		mv ${i}{,2} || die
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	done
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	popd >/dev/null || die
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}
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pkg_postinst() {
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	elog "All ${P} binaries have been renamed, in order"
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	elog "to avoid collisions with hmmer-3. For instance"
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	elog
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	elog "    hmmalign -> hmmalign2"
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	elog
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	insinto /usr/share/${PN}
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	doins -r tutorial
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}
Thank you!