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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-04-23 01:04:03 +0200
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-04-23 01:04:03 +0200
commit57485834b37ce2b2da440ee2befb0c92abc725d5 (patch)
tree0a664de75fd4fd334b328f0c7122a09c17ad0891 /sci-biology/kat/kat-2.4.1.ebuild
parentsci-biology/megahit: respect cuda USE flag (diff)
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sci-biology/kat: properly install python files
Thanks to kiwifb. Drop -8888, update -9999 and -2.4.1 to link against system-wide boost. No ebuilds left which would let the bundled boost slip in as a static library. See: https://github.com/TGAC/KAT/issues/94#issuecomment-383385701 Closes: https://github.com/gentoo/sci/issues/867 Package-Manager: Portage-2.3.31, Repoman-2.3.9
Diffstat (limited to 'sci-biology/kat/kat-2.4.1.ebuild')
-rw-r--r--sci-biology/kat/kat-2.4.1.ebuild44
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
}