diff options
Diffstat (limited to 'sci-biology/kat/kat-9999.ebuild')
| -rw-r--r-- | sci-biology/kat/kat-9999.ebuild | 60 |
1 files changed, 36 insertions, 24 deletions
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild index 0ccec1481..aaf8842ba 100644 --- a/sci-biology/kat/kat-9999.ebuild +++ b/sci-biology/kat/kat-9999.ebuild @@ -3,57 +3,65 @@ EAPI=6 -PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 +PYTHON_COMPAT=( python3_{5,6} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30 -inherit git-r3 eutils flag-o-matic autotools distutils-r1 +inherit flag-o-matic autotools distutils-r1 git-r3 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" HOMEPAGE="https://github.com/TGAC/KAT" EGIT_REPO_URI="https://github.com/TGAC/KAT.git" +EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}" LICENSE="GPL-3+" SLOT="0" -KEYWORDS="" -IUSE="cpu_flags_x86_sse doc tex" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse static-libs test" -DEPEND=" +CDEPEND=" >=dev-libs/boost-1.52[${PYTHON_USEDEP}] + sys-libs/zlib dev-python/tabulate[${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="${DEPEND}" -# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) -# contains embedded sci-biology/seqan + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND="${CDEPEND} + dev-python/sphinx + test? ( sys-process/time )" +RDEPEND="${CDEPEND}" +# contains bundled and *modified* version of jellyfish-2.2.0 +# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) +# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 +# contains embedded sci-biology/seqan headers + +PATCHES=( + "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch + "${FILESDIR}"/kat-2.4.2-no_static_build.patch + ) + +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(){ + python_setup 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 + myconf+=( + --disable-gnuplot + --disable-pykat-install + $(use_enable static-libs static) + ) # python3 does better image rendering, no need for gnuplot + # pass down to jellyfish-2.2.0/configure + use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) econf ${myconf[@]} } src_compile(){ - emake - cd doc && make latexpdf && cd .. || die + default pushd scripts >/dev/null || die distutils-r1_src_compile popd > /dev/null || die @@ -65,3 +73,7 @@ src_install(){ distutils-r1_src_install popd > /dev/null || die } + +src_test(){ + default +} |