1 files changed, 0 insertions, 81 deletions
diff --git a/sci-biology/tophat/tophat-2.1.1-r4.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild
deleted file mode 100644
index 590f6eb2d20f..000000000000
--- a/sci-biology/tophat/tophat-2.1.1-r4.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# 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
-}