1 files changed, 0 insertions, 61 deletions
diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild
deleted file mode 100644
index 6625162e2..000000000
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
-HOMEPAGE="http://ccb.jhu.edu/software/tophat"
-# https://github.com/infphilo/tophat
-# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
-SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-#   samtools_0.1.18 view -h -
-#   samtools_0.1.18 sort
-#   samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
-	>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
-
-# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die
-	sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
-	# rm -rf src/SeqAn* || die
-	eautoreconf
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-	cd ../"${P}"_build/src || die
-	ln -s ../"${P}"/src/SeqAn-1.3 . || die
-	ln -s ../../"${P}"/src/samtools-0.1.18 . || die
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die
-}
-
-src_install() {
-	# introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
-	sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
-	autotools-utils_src_install
-	python_fix_shebang "${ED}"/usr/bin/tophat
-}