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55 lines
1.2 KiB
55 lines
1.2 KiB
# Copyright 1999-2017 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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PYTHON_COMPAT=( python2_7 )
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inherit autotools flag-o-matic python-single-r1 toolchain-funcs
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DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq"
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HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
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SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
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LICENSE="Artistic"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="debug"
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REQUIRED_USE="${PYTHON_REQUIRED_USE}"
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RDEPEND="
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sci-biology/samtools:0.1-legacy
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>=dev-libs/boost-1.62.0:=
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${PYTHON_DEPS}"
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DEPEND="
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${RDEPEND}
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dev-cpp/eigen:3
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virtual/pkgconfig"
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PATCHES=(
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"${FILESDIR}"/${P}-samtools-legacy.patch
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"${FILESDIR}"/${P}-flags.patch
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"${FILESDIR}"/${P}-gcc6.patch
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"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
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)
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src_prepare() {
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default
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python_fix_shebang src/cuffmerge
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eautoreconf
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}
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src_configure() {
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# keep in sync with Boost
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append-cxxflags -std=c++14
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append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
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econf \
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--disable-optim \
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--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
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--with-bam="${EPREFIX}/usr/" \
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$(use_enable debug) \
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PYTHON="${PYTHON}"
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}
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