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author | V3n3RiX <venerix@redcorelinux.org> | 2020-02-29 18:01:47 +0000 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2020-02-29 18:01:47 +0000 |
commit | ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (patch) | |
tree | 9f47ee47c31a0f13f9496879cd88a1042550aa81 /sci-biology/tophat/tophat-2.1.1-r5.ebuild | |
parent | 53cba99042fa967e2a93da9f8db806fe2d035543 (diff) |
gentoo (leap year) resync : 29.02.2020
Diffstat (limited to 'sci-biology/tophat/tophat-2.1.1-r5.ebuild')
-rw-r--r-- | sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 |
1 files changed, 0 insertions, 83 deletions
diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild deleted file mode 100644 index 753188771381..000000000000 --- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools eutils 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] - $(python_gen_cond_dep ' - dev-python/intervaltree[${PYTHON_MULTI_USEDEP}] - dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}] - ') - sci-biology/samtools:0.1-legacy - sci-biology/bowtie:2" -DEPEND="${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 -} |