commit: 9d6fa783c4d323bddcc63ae47a2c8c3c2d47580e Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Apr 21 15:25:37 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Apr 21 15:25:37 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d6fa783
sci-biology/kat: version bump Lets require >=python-3.5 for best feature availability. The source code contain bundled sci-libs/boost and sci-biology/seqan. It also contain (unfortunately modified) sci-biology/jellyfish-2.2.0 https://github.com/TGAC/KAT/issues/92 Package-Manager: Portage-2.3.28, Repoman-2.3.9 sci-biology/kat/kat-2.2.0.ebuild | 31 ---------------------------- sci-biology/kat/kat-2.4.1.ebuild | 44 ++++++++++++++++++++++++++++++++++++++++ sci-biology/kat/kat-9999.ebuild | 18 ++++++++-------- 3 files changed, 54 insertions(+), 39 deletions(-) diff --git a/sci-biology/kat/kat-2.2.0.ebuild b/sci-biology/kat/kat-2.2.0.ebuild deleted file mode 100644 index 396d9cc4a..000000000 --- a/sci-biology/kat/kat-2.2.0.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit python-r1 eutils flag-o-matic - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT"; -SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz"; - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="cpu_flags_x86_sse" - -DEPEND="dev-libs/boost:0 - dev-python/matplotlib - sci-visualization/gnuplot" -RDEPEND="${DEPEND}" -# contains bundled modified version of jellyfish-2.2 which should install under different filenames - -src_configure(){ - local myconf=() - myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure - PYTHON_VERSION=3 econf ${myconf[@]} - eapply_user -} diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild new file mode 100644 index 000000000..466b5431e --- /dev/null +++ b/sci-biology/kat/kat-2.4.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 +# https://github.com/Ensembl/Bio-DB-HTS/issues/30 + +inherit python-r1 eutils flag-o-matic + +DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" +HOMEPAGE="https://github.com/TGAC/KAT"; +SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="cpu_flags_x86_sse doc" + +DEPEND=" + >=dev-libs/boost-1.52 + dev-python/tabulate + dev-python/matplotlib + dev-python/numpy + sci-libs/scipy + doc? ( dev-python/sphinx )" +RDEPEND="${DEPEND}" +# contains bundled *modified* version of jellyfish-2.2 which should install under different filenames +# contains embedded sci-biology/seqan + +S="${WORKDIR}"/KAT-Release-"${PV}" + +src_prepare(){ + default + sh build_boost.sh || die + sh autogen.sh || die +} + +src_configure(){ + local myconf=() + myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot + use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure + PYTHON_VERSION=3 econf ${myconf[@]} +} diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild index 4290739f5..39107167a 100644 --- a/sci-biology/kat/kat-9999.ebuild +++ b/sci-biology/kat/kat-9999.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1 +PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 +# https://github.com/Ensembl/Bio-DB-HTS/issues/30 inherit git-r3 eutils flag-o-matic @@ -14,23 +15,24 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git"; LICENSE="GPL-3+" SLOT="0" KEYWORDS="" -IUSE="cpu_flags_x86_sse" +IUSE="cpu_flags_x86_sse doc" DEPEND=" - dev-lang/python:3 >=dev-libs/boost-1.52 + dev-python/tabulate dev-python/matplotlib dev-python/numpy sci-libs/scipy - dev-python/sphinx" + doc? ( dev-python/sphinx )" RDEPEND="${DEPEND}" -# contains bundled a modified version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) +# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) +# contains embedded sci-biology/seqan src_prepare(){ - sh ./autogen.sh . || die + sh build_boost.sh || die + sh autogen.sh . || die local myconf=() myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure PYTHON_VERSION=3 econf ${myconf[@]} - eapply_user }
