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70 lines
1.7 KiB
70 lines
1.7 KiB
9 years ago
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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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# $Id$
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EAPI=6
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PYTHON_COMPAT=( python2_7 )
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inherit autotools eutils flag-o-matic python-single-r1
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DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
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HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
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SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
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LICENSE="Artistic"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="debug"
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RDEPEND="dev-libs/boost
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sci-biology/samtools:0.1-legacy
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sci-biology/bowtie:2"
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DEPEND="${RDEPEND}
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sci-biology/seqan:1.4"
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PATCHES=(
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"${FILESDIR}/${P}-unbundle-seqan-samtools.patch"
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)
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src_prepare() {
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default
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# remove bundled libs
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rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
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sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
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-i src/tophat.py src/common.cpp || die
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sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
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-e '/^samtools-0\.1\.18\//d' \
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-e '/^SeqAn-1\.4\.2\//d' \
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-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
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-e 's:\$(top_builddir)\/src\/::' \
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-i src/Makefile.am || die
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sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
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# innocuous non-security flags, prevent log pollution
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append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
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append-cppflags "$(pkg-config --cflags seqan-1.4)"
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eautoreconf
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}
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src_configure() {
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econf $(use_enable debug)
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}
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src_install() {
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default
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local i
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for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do
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python_fix_shebang "${ED}"/usr/bin/${i}
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done
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}
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pkg_postinst() {
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optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
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}
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