commit: 2e9f85acc8a4dfe99a06aeef66b0cc3eb4416799 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Apr 21 16:21:46 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Apr 21 16:21:46 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e9f85ac
sci-biology/sailfish: drop KEYWORDS, version bump This package automatically downloads 3rd-party sources instead of just compiling. https://github.com/kingsfordgroup/sailfish/issues/80 Package-Manager: Portage-2.3.28, Repoman-2.3.9 .../{sailfish-0.9.2.ebuild => sailfish-0.10.0.ebuild} | 19 ++++++++++--------- sci-biology/sailfish/sailfish-9999.ebuild | 18 ++++++++++++++---- 2 files changed, 24 insertions(+), 13 deletions(-) diff --git a/sci-biology/sailfish/sailfish-0.9.2.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild similarity index 64% rename from sci-biology/sailfish/sailfish-0.9.2.ebuild rename to sci-biology/sailfish/sailfish-0.10.0.ebuild index d4953a2a5..9d618076d 100644 --- a/sci-biology/sailfish/sailfish-0.9.2.ebuild +++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 -inherit cmake-utils +inherit cmake-utils multilib DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"; @@ -11,27 +11,28 @@ SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.t LICENSE="GPL-3+" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +KEYWORDS="" IUSE="" PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) DEPEND="dev-libs/boost:0 dev-libs/jemalloc - dev-cpp/tbb" + dev-cpp/tbb + sci-biology/jellyfish:2" RDEPEND="${DEPEND}" # a C++-11 compliant compiler is needs, aka >=gcc-4.7 -# TODO: disable -# [ 7%] Performing download step (verify and extract) for 'libdivsufsort' -#i +# TODO: disable running wget/curl during src_compile +# https://github.com/kingsfordgroup/sailfish/issues/80 # contains bundled RapMap -# contains bundled libdivsufsort-master +# contains bundled libdivsufsort # contains bundled libgff # contains bundled jellyfish-2.2.3 -# contains bundled sparsehash-sparsehash-2.0.2 +# contains bundled sparsehash-2.0.2 src_install() { cmake-utils_src_install rm -r "${ED}"/usr/tests || die + rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die } diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild index 6c37b858e..f31f16197 100644 --- a/sci-biology/sailfish/sailfish-9999.ebuild +++ b/sci-biology/sailfish/sailfish-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 -inherit cmake-utils git-r3 +inherit cmake-utils git-r3 multilib DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"; @@ -14,14 +14,24 @@ LICENSE="GPL-3" SLOT="0" IUSE="" -PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch ) +PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch ) DEPEND="dev-libs/boost:0 dev-libs/jemalloc - dev-cpp/tbb" + dev-cpp/tbb + sci-biology/jellyfish:2" RDEPEND="${DEPEND}" +# TODO: disable running wget/curl during src_compile +# https://github.com/kingsfordgroup/sailfish/issues/80 +# contains bundled RapMap +# contains bundled libdivsufsort-master +# contains bundled libgff +# contains bundled jellyfish-2.2.3 +# contains bundled sparsehash-2.0.2 + src_install() { cmake-utils_src_install rm -r "${ED}"/usr/tests || die + rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die }
