| # Copyright 1999-2017 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| |
| EAPI=6 |
| |
| PYTHON_COMPAT=( python2_7 ) |
| |
| inherit autotools flag-o-matic python-single-r1 toolchain-funcs |
| |
| DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" |
| HOMEPAGE="https://ccb.jhu.edu/software/tophat/" |
| SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" |
| |
| LICENSE="Artistic" |
| SLOT="0" |
| KEYWORDS="~amd64 ~x86" |
| IUSE="debug" |
| REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| |
| RDEPEND="${PYTHON_DEPS} |
| dev-libs/boost:=[threads] |
| dev-python/intervaltree[${PYTHON_USEDEP}] |
| dev-python/sortedcontainers[${PYTHON_USEDEP}] |
| sci-biology/samtools:0.1-legacy |
| sci-biology/bowtie:2" |
| DEPEND="${RDEPEND} |
| virtual/pkgconfig |
| sci-biology/seqan:1.4 |
| >=sys-devel/autoconf-archive-2016.09.16" |
| |
| PATCHES=( |
| "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch |
| "${FILESDIR}"/${P}-fix-c++14.patch |
| "${FILESDIR}"/${P}-python2-shebangs.patch |
| ) |
| |
| src_prepare() { |
| default |
| |
| # remove bundled libs |
| rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die |
| |
| sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ |
| -i src/tophat.py src/common.cpp || die |
| |
| sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ |
| -e '/^samtools-0\.1\.18\//d' \ |
| -e '/^SeqAn-1\.4\.2\//d' \ |
| -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ |
| -e 's:\$(top_builddir)\/src\/::' \ |
| -i src/Makefile.am || die |
| sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die |
| |
| # innocuous non-security flags, prevent log pollution |
| append-cflags -Wno-unused-but-set-variable -Wno-unused-variable |
| append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" |
| |
| # remove ancient autoconf archive macros, wreaking havoc, |
| # depend on sys-devel/autoconf-archive instead, bug #594810 |
| rm {ax_boost_thread,ax_boost_base}.m4 || die |
| |
| eautoreconf |
| } |
| |
| src_configure() { |
| econf $(use_enable debug) |
| } |
| |
| src_install() { |
| default |
| |
| # delete bundled python modules |
| local i |
| for i in intervaltree sortedcontainers; do |
| rm -r "${ED%/}"/usr/bin/${i} || die |
| done |
| } |
| |
| pkg_postinst() { |
| optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 |
| } |