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Diffstat (limited to 'sci-biology/kat/kat-2.4.1.ebuild')
-rw-r--r--sci-biology/kat/kat-2.4.1.ebuild69
1 files changed, 0 insertions, 69 deletions
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
deleted file mode 100644
index 3bd8b7dde..000000000
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# 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 eutils flag-o-matic autotools distutils-r1
-
-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-2.4.1.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse doc tex"
-
-DEPEND="
- >=dev-libs/boost-1.52[${PYTHON_USEDEP}]
- dev-python/tabulate[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- sci-libs/scipy[${PYTHON_USEDEP}]
- doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
- tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
-RDEPEND="${DEPEND}"
-# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so})
-# contains embedded sci-biology/seqan
-
-S="${WORKDIR}"/KAT-Release-"${PV}"
-
-src_prepare(){
- default
- # keep bundled seqan-library-2.0.0 jellyfish-2.2.0
- # seqan header do not hurt
- # jellyfish-2.2.0 is a modified version, "kat_" prefixes are added to all binaries
- # https://github.com/TGAC/KAT/issues/93#issuecomment-383377666
- rm -rf deps/boost || die "Failed to zap bundled boost"
- epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch
- epatch "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch
- eautoreconf
- pushd scripts >/dev/null || die
- distutils-r1_src_prepare
- popd > /dev/null || 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-2.2.0/configure
- econf ${myconf[@]}
-}
-
-src_compile(){
- emake
- cd doc && make latexpdf && cd .. || die
- pushd scripts >/dev/null || die
- distutils-r1_src_compile
- popd > /dev/null || die
-}
-
-src_install(){
- default
- pushd scripts >/dev/null || die
- distutils-r1_src_install
- popd > /dev/null || die
-}