1 files changed, 0 insertions, 83 deletions
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
deleted file mode 100644
index 8ba4d0cf7..000000000
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake multilib
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
-	https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
-	https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
-	https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
-"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
-	dev-libs/boost:0
-	dev-libs/jemalloc
-	dev-libs/libdivsufsort
-	dev-cpp/tbb
-	dev-cpp/sparsehash
-	sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-BDEPEND="app-arch/unzip"
-# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.9.2-no-boost-static.patch"
-	"${FILESDIR}/${PN}-no-curl.patch"
-	"${FILESDIR}/${PN}-allow-newer-boost.patch"
-)
-
-src_unpack() {
-	default
-	mkdir -p "${S}/external"
-	cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
-	mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
-	mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
-	mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
-	mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
-	mkdir -p "${S}/external/install/lib"
-	cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
-	cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
-	cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
-	mkdir -p "${S}/external/install/src/rapmap"
-	cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-	# use the dynamic library
-	sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
-		-e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
-		-e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
-		src/CMakeLists.txt || die
-}
-
-src_configure() {
-	JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure
-	# jellyfish2 instead of jellyfish
-	find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die
-	find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die
-}
-
-src_install() {
-	cmake_src_install
-	rm -r "${ED}"/usr/tests || die
-	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}