aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat (limited to 'sci-biology/kat/kat-9999.ebuild')
-rw-r--r--sci-biology/kat/kat-9999.ebuild60
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
+}