diff options
Diffstat (limited to 'sci-biology/kat/kat-2.4.1.ebuild')
| -rw-r--r-- | sci-biology/kat/kat-2.4.1.ebuild | 44 |
1 files changed, 28 insertions, 16 deletions
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild index 86dd7b5a8..3bd8b7dde 100644 --- a/sci-biology/kat/kat-2.4.1.ebuild +++ b/sci-biology/kat/kat-2.4.1.ebuild @@ -6,15 +6,15 @@ 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 +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-${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/TGAC/KAT/archive/Release-2.4.1.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3+" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse doc tex" DEPEND=" @@ -26,32 +26,44 @@ DEPEND=" doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )" RDEPEND="${DEPEND}" -# contains bundled *modified* version of jellyfish-2.2 which should install under different filenames +# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) # contains embedded sci-biology/seqan S="${WORKDIR}"/KAT-Release-"${PV}" src_prepare(){ default - # autogen.sh - test -n "$srcdir" || local srcdir=`dirname "$0"` - test -n "$srcdir" || local srcdir=. - eautoreconf --force --install --verbose "$srcdir" + # keep bundled seqan-library-2.0.0 jellyfish-2.2.0 + # seqan header do not hurt + # jellyfish-2.2.0 is a modified version, "kat_" prefixes are added to all binaries + # https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 + rm -rf deps/boost || die "Failed to zap bundled boost" + epatch "${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 - PYTHON_VERSION=3 econf ${myconf[@]} + econf ${myconf[@]} } src_compile(){ - # build_boost.sh - cd deps/boost || die - ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die - # https://github.com/TGAC/KAT/issues/92#issuecomment-383373418 - ./b2 headers --ignore-site-config || die - ./b2 install --ignore-site-config || die - cd ../.. || die + 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 } |