1 files changed, 0 insertions, 62 deletions
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
deleted file mode 100644
index a76e8ee89..000000000
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" )
-
-DEPEND="
-	dev-libs/boost:0
-	dev-libs/jemalloc
-	dev-libs/libdivsufsort
-	dev-cpp/tbb
-	sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_unpack() {
-	default
-	mkdir -p "${S}/external"
-	cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || 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
-}
-
-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
-
-	# jellyfish2 instead of jellyfish
-	pushd external/install/include/rapmap
-	find -type f -name "*.hpp" -exec sed -i -e 's/jellyfish/jellyfish2/g' {} + || die
-	popd
-}
-
-src_install() {
-	cmake_src_install
-	rm -r "${ED}"/usr/tests || die
-	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}