* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2016-10-17 15:21 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-10-17 15:21 UTC (permalink / raw
To: gentoo-commits
commit: 02cb4dded41609783964b8a0f6d01dde60455535
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Oct 17 15:21:39 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Oct 17 15:21:39 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=02cb4dde
sci-biology/kat: new package
Boost library is not found during linking step
Package needs >=python-3.1 as the default python interpreter (for what?)
The bundled jellyfish code seems to result in a renamed library and *.pc
file so probably it will not clash with system-wide jellyfish
Package-Manager: portage-2.3.0
sci-biology/kat/kat-2.1.1.ebuild | 29 +++++++++++++++++++++++++++++
sci-biology/kat/kat-9999.ebuild | 29 +++++++++++++++++++++++++++++
sci-biology/kat/metadata.xml | 12 ++++++++++++
3 files changed, 70 insertions(+)
diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.1.1.ebuild
new file mode 100644
index 0000000..3a184c9
--- /dev/null
+++ b/sci-biology/kat/kat-2.1.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+
+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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-libs/boost:0
+ dev-python/matplotlib
+ sci-visualization/gnuplot"
+RDEPEND="${DEPEND}"
+# contains bundled modified version of jellyfish-2.2.
+
+S="${WORKDIR}"/KAT-Release-"${PV}"
+
+src_prepare(){
+ sh ./autogen.sh . || die
+ default
+}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
new file mode 100644
index 0000000..e8735e4
--- /dev/null
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+
+inherit 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"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-libs/boost:0
+ dev-python/matplotlib
+ sci-visualization/gnuplot"
+RDEPEND="${DEPEND}"
+# contains bundled a modified version of jellyfish-2.2.0
+
+src_prepare(){
+ sh ./autogen.sh . || die
+ default
+}
diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/kat/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2016-10-17 16:46 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-10-17 16:46 UTC (permalink / raw
To: gentoo-commits
commit: 4df5011f6c061f637cfb0cd3629a5f0a8fcc25de
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Oct 17 16:46:05 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Oct 17 16:46:05 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4df5011f
sci-biology/kat: fix SRC_URI
use SRC_URI for a real release, not for an automatically generated github tarball (upstream issue #59)
Package-Manager: portage-2.3.0
sci-biology/kat/kat-2.1.1.ebuild | 9 +--------
1 file changed, 1 insertion(+), 8 deletions(-)
diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.1.1.ebuild
index 3a184c9..8133fdb 100644
--- a/sci-biology/kat/kat-2.1.1.ebuild
+++ b/sci-biology/kat/kat-2.1.1.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
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 -> ${P}.tar.gz"
+SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
@@ -20,10 +20,3 @@ DEPEND="dev-libs/boost:0
sci-visualization/gnuplot"
RDEPEND="${DEPEND}"
# contains bundled modified version of jellyfish-2.2.
-
-S="${WORKDIR}"/KAT-Release-"${PV}"
-
-src_prepare(){
- sh ./autogen.sh . || die
- default
-}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2016-11-30 22:33 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-11-30 22:33 UTC (permalink / raw
To: gentoo-commits
commit: 1d87d213225badbbf304e163a61815219052cca4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Nov 30 22:33:40 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Nov 30 22:33:40 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d87d213
sci-biology/kat: version bump, blocked by upstream issue #61
Package-Manager: portage-2.3.2
sci-biology/kat/{kat-2.1.1.ebuild => kat-2.2.0.ebuild} | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
similarity index 62%
rename from sci-biology/kat/kat-2.1.1.ebuild
rename to sci-biology/kat/kat-2.2.0.ebuild
index 8133fdb..38ddae2 100644
--- a/sci-biology/kat/kat-2.1.1.ebuild
+++ b/sci-biology/kat/kat-2.2.0.ebuild
@@ -4,7 +4,9 @@
EAPI=6
-PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30
+
+inherit python-r1
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
@@ -19,4 +21,8 @@ DEPEND="dev-libs/boost:0
dev-python/matplotlib
sci-visualization/gnuplot"
RDEPEND="${DEPEND}"
-# contains bundled modified version of jellyfish-2.2.
+# contains bundled modified version of jellyfish-2.2 which should install under different filenames
+
+src_configure(){
+ econf PYTHON_VERSION="${PYTHON_SINGLE_TARGET}"
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2016-12-09 16:26 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-12-09 16:26 UTC (permalink / raw
To: gentoo-commits
commit: d8e71f09ea2222b8f04e79adb3f1772e680a0a24
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 9 16:26:07 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 9 16:26:07 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8e71f09
sci-biology/kat: respect sse CPU USE flags
Package-Manager: portage-2.3.3
sci-biology/kat/kat-2.2.0.ebuild | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/kat/kat-2.2.0.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
index 38ddae2..fbd3834 100644
--- a/sci-biology/kat/kat-2.2.0.ebuild
+++ b/sci-biology/kat/kat-2.2.0.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30
-inherit python-r1
+inherit python-r1 eutils flag-o-matic
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
@@ -15,7 +15,7 @@ SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="cpu_flags_x86_sse"
DEPEND="dev-libs/boost:0
dev-python/matplotlib
@@ -24,5 +24,9 @@ RDEPEND="${DEPEND}"
# contains bundled modified version of jellyfish-2.2 which should install under different filenames
src_configure(){
- econf PYTHON_VERSION="${PYTHON_SINGLE_TARGET}"
+ 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-2.20/configure
+ PYTHON_VERSION=3 econf ${myconf[@]}
+ eapply_user
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2016-12-09 16:26 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-12-09 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 25e7181982a0e06eab199571be8765db4633591c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 9 16:24:23 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 9 16:24:23 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=25e71819
sci-biology/kat:
Package-Manager: portage-2.3.3
sci-biology/kat/kat-9999.ebuild | 20 ++++++++++++++------
1 file changed, 14 insertions(+), 6 deletions(-)
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index e8735e4..782d3fc 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
-inherit git-r3
+inherit git-r3 eutils flag-o-matic
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
@@ -15,15 +15,23 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="cpu_flags_x86_sse"
-DEPEND="dev-libs/boost:0
+DEPEND="
+ dev-lang/python:3
+ >=dev-libs/boost-1.52
dev-python/matplotlib
- sci-visualization/gnuplot"
+ dev-python/numpy
+ sci-libs/scipy
+ dev-python/sphinx"
RDEPEND="${DEPEND}"
-# contains bundled a modified version of jellyfish-2.2.0
+# contains bundled a modified version of jellyfish-2.2.0 (libkat_jellyfish.{a,so})
src_prepare(){
sh ./autogen.sh . || die
- default
+ 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-2.20/configure
+ PYTHON_VERSION=3 econf ${myconf[@]}
+ eapply_user
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2018-04-21 15:26 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-04-21 15:26 UTC (permalink / raw
To: gentoo-commits
commit: 9d6fa783c4d323bddcc63ae47a2c8c3c2d47580e
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 15:25:37 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 15:25:37 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d6fa783
sci-biology/kat: version bump
Lets require >=python-3.5 for best feature availability.
The source code contain bundled sci-libs/boost and
sci-biology/seqan.
It also contain (unfortunately modified) sci-biology/jellyfish-2.2.0
https://github.com/TGAC/KAT/issues/92
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/kat/kat-2.2.0.ebuild | 31 ----------------------------
sci-biology/kat/kat-2.4.1.ebuild | 44 ++++++++++++++++++++++++++++++++++++++++
sci-biology/kat/kat-9999.ebuild | 18 ++++++++--------
3 files changed, 54 insertions(+), 39 deletions(-)
diff --git a/sci-biology/kat/kat-2.2.0.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
deleted file mode 100644
index 396d9cc4a..000000000
--- a/sci-biology/kat/kat-2.2.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit python-r1 eutils flag-o-matic
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE="cpu_flags_x86_sse"
-
-DEPEND="dev-libs/boost:0
- dev-python/matplotlib
- sci-visualization/gnuplot"
-RDEPEND="${DEPEND}"
-# contains bundled modified version of jellyfish-2.2 which should install under different filenames
-
-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-2.20/configure
- PYTHON_VERSION=3 econf ${myconf[@]}
- eapply_user
-}
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
new file mode 100644
index 000000000..466b5431e
--- /dev/null
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
+# https://github.com/Ensembl/Bio-DB-HTS/issues/30
+
+inherit python-r1 eutils flag-o-matic
+
+DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
+HOMEPAGE="https://github.com/TGAC/KAT"
+SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE="cpu_flags_x86_sse doc"
+
+DEPEND="
+ >=dev-libs/boost-1.52
+ dev-python/tabulate
+ dev-python/matplotlib
+ dev-python/numpy
+ sci-libs/scipy
+ doc? ( dev-python/sphinx )"
+RDEPEND="${DEPEND}"
+# contains bundled *modified* version of jellyfish-2.2 which should install under different filenames
+# contains embedded sci-biology/seqan
+
+S="${WORKDIR}"/KAT-Release-"${PV}"
+
+src_prepare(){
+ default
+ sh build_boost.sh || die
+ sh autogen.sh || 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-2.20/configure
+ PYTHON_VERSION=3 econf ${myconf[@]}
+}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 4290739f5..39107167a 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
+# https://github.com/Ensembl/Bio-DB-HTS/issues/30
inherit git-r3 eutils flag-o-matic
@@ -14,23 +15,24 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
-IUSE="cpu_flags_x86_sse"
+IUSE="cpu_flags_x86_sse doc"
DEPEND="
- dev-lang/python:3
>=dev-libs/boost-1.52
+ dev-python/tabulate
dev-python/matplotlib
dev-python/numpy
sci-libs/scipy
- dev-python/sphinx"
+ doc? ( dev-python/sphinx )"
RDEPEND="${DEPEND}"
-# contains bundled a modified version of jellyfish-2.2.0 (libkat_jellyfish.{a,so})
+# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so})
+# contains embedded sci-biology/seqan
src_prepare(){
- sh ./autogen.sh . || die
+ sh build_boost.sh || die
+ sh autogen.sh . || die
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-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
- eapply_user
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2018-04-22 8:58 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-04-22 8:58 UTC (permalink / raw
To: gentoo-commits
commit: aca4c5886f2dc4991a59805666245be2a627f0ea
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 08:57:59 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 08:57:59 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=aca4c588
sci-biology/kat: execute the build_boost.sh and autogen.sh logic
Execute the commands from within ebuild to ease debugging of errors.
See https://github.com/TGAC/KAT/issues/92
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/kat/kat-2.4.1.ebuild | 15 +++++++++++++--
sci-biology/kat/kat-9999.ebuild | 21 ++++++++++++++++++---
2 files changed, 31 insertions(+), 5 deletions(-)
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 466b5431e..1df9f4430 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -32,8 +32,10 @@ S="${WORKDIR}"/KAT-Release-"${PV}"
src_prepare(){
default
- sh build_boost.sh || die
- sh autogen.sh || die
+ # autogen.sh
+ test -n "$srcdir" || local srcdir=`dirname "$0"`
+ test -n "$srcdir" || local srcdir=.
+ eautoreconf --force --install --verbose "$srcdir"
}
src_configure(){
@@ -42,3 +44,12 @@ src_configure(){
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
}
+
+src_compile(){
+ # build_boost.sh
+ cd deps/boost || die
+ ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
+ ./b2 headers || die
+ ./b2 install || die
+ cd ../.. || die
+}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 39107167a..d46f6d3e8 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-inherit git-r3 eutils flag-o-matic
+inherit git-r3 eutils flag-o-matic autotools
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
@@ -29,10 +29,25 @@ RDEPEND="${DEPEND}"
# contains embedded sci-biology/seqan
src_prepare(){
- sh build_boost.sh || die
- sh autogen.sh . || die
+ default
+ # autogen.sh
+ test -n "$srcdir" || local srcdir=`dirname "$0"`
+ test -n "$srcdir" || local srcdir=.
+ eautoreconf --force --install --verbose "$srcdir"
+}
+
+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-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
}
+
+src_compile(){
+ # build_boost.sh
+ cd deps/boost || die
+ ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
+ ./b2 headers || die
+ ./b2 install || die
+ cd ../.. || die
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2018-04-22 11:57 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-04-22 11:57 UTC (permalink / raw
To: gentoo-commits
commit: fb4f6614269a5413ca8d03aeb6707aabad9ec8cb
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 11:56:50 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 11:57:19 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fb4f6614
sci-biology/kat: remove lines commented out
Package-Manager: Portage-2.3.28, Repoman-2.3.9
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/kat/kat-8888.ebuild | 12 ------------
1 file changed, 12 deletions(-)
diff --git a/sci-biology/kat/kat-8888.ebuild b/sci-biology/kat/kat-8888.ebuild
index c59669fc5..2c88b2a25 100644
--- a/sci-biology/kat/kat-8888.ebuild
+++ b/sci-biology/kat/kat-8888.ebuild
@@ -33,9 +33,6 @@ src_prepare(){
rm -rf deps || die "Failed to zap bundled seqan-library-2.0.0 jellyfish-2.2.0 boost"
epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch
epatch "${FILESDIR}"/kat-2.4.1-rename-jellyfish.patch
- # autogen.sh
- #test -n "$srcdir" || local srcdir=`dirname "$0"`
- #test -n "$srcdir" || local srcdir=.
eautoreconf --force --install --verbose "$srcdir"
}
@@ -45,12 +42,3 @@ src_configure(){
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
}
-
-#src_compile(){
-# # build_boost.sh
-# cd deps/boost || die
-# ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
-# ./b2 headers --prefix=build || die
-# ./b2 install --prefix=build || die
-# cd ../.. || die
-#}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2018-04-22 21:18 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-04-22 21:18 UTC (permalink / raw
To: gentoo-commits
commit: 65304d57d4c51cdf0c55740ee37f30e800090a16
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 21:17:51 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 21:17:51 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=65304d57
sci-biology/kat: add missing DEPENDency
Package-Manager: Portage-2.3.31, Repoman-2.3.9
sci-biology/kat/kat-2.4.1.ebuild | 5 +++--
sci-biology/kat/kat-8888.ebuild | 2 +-
sci-biology/kat/kat-9999.ebuild | 5 +++--
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 29f11c9f6..86dd7b5a8 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -15,7 +15,7 @@ SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc"
+IUSE="cpu_flags_x86_sse doc tex"
DEPEND="
>=dev-libs/boost-1.52[${PYTHON_USEDEP}]
@@ -23,7 +23,8 @@ DEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
- doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
+ 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 embedded sci-biology/seqan
diff --git a/sci-biology/kat/kat-8888.ebuild b/sci-biology/kat/kat-8888.ebuild
index a8a776c29..07c3f57d2 100644
--- a/sci-biology/kat/kat-8888.ebuild
+++ b/sci-biology/kat/kat-8888.ebuild
@@ -24,7 +24,7 @@ DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
- tex? ( dev-tex/latexmk )"
+ tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
RDEPEND="${DEPEND}"
# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so})
# contains embedded sci-biology/seqan
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 8fe79a34b..403a0df59 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -15,7 +15,7 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc"
+IUSE="cpu_flags_x86_sse doc tex"
DEPEND="
>=dev-libs/boost-1.52
@@ -23,7 +23,8 @@ DEPEND="
dev-python/matplotlib
dev-python/numpy
sci-libs/scipy
- doc? ( dev-python/sphinx )"
+ doc? ( dev-python/sphinx )
+ 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
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2018-04-22 23:04 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-04-22 23:04 UTC (permalink / raw
To: gentoo-commits
commit: 57485834b37ce2b2da440ee2befb0c92abc725d5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 23:04:03 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 23:04:03 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57485834
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
sci-biology/kat/kat-2.4.1.ebuild | 44 ++++++++++++++++---------
sci-biology/kat/kat-8888.ebuild | 70 ----------------------------------------
sci-biology/kat/kat-9999.ebuild | 50 +++++++++++++++++-----------
3 files changed, 59 insertions(+), 105 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 ${myconf[@]}
}
src_compile(){
- # build_boost.sh
- cd deps/boost || die
- ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
- # https://github.com/TGAC/KAT/issues/92#issuecomment-383373418
- ./b2 headers --ignore-site-config || die
- ./b2 install --ignore-site-config || die
- cd ../.. || die
+ emake
+ cd doc && make latexpdf && cd .. || die
+ pushd scripts >/dev/null || die
+ distutils-r1_src_compile
+ popd > /dev/null || die
+}
+
+src_install(){
+ default
+ pushd scripts >/dev/null || die
+ distutils-r1_src_install
+ popd > /dev/null || die
}
diff --git a/sci-biology/kat/kat-8888.ebuild b/sci-biology/kat/kat-8888.ebuild
deleted file mode 100644
index 07c3f57d2..000000000
--- a/sci-biology/kat/kat-8888.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit git-r3 eutils flag-o-matic autotools distutils-r1
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc tex"
-
-DEPEND="
- >=dev-libs/boost-1.52[${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
-
-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
-}
-
-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-2.20/configure
- econf ${myconf[@]}
-}
-
-src_compile(){
- emake
- cd doc && make latexpdf || die
-}
-
-src_install(){
- # emake install
- default
- # install python files (the "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch
- # removed code which ignored ${DESTDIR})
- # https://github.com/TGAC/KAT/issues/94#issuecomment-383385701
- cd scripts || die
- esetup.py install --record install_files.txt
-}
-
-# probably the below is not needed (does not seem to work)
-python_install_all() {
- cd scripts || die
- distutils-r1_python_install_all
-}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 403a0df59..0ccec1481 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-inherit git-r3 eutils flag-o-matic autotools
+inherit git-r3 eutils flag-o-matic autotools distutils-r1
DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
HOMEPAGE="https://github.com/TGAC/KAT"
@@ -18,12 +18,12 @@ KEYWORDS=""
IUSE="cpu_flags_x86_sse doc tex"
DEPEND="
- >=dev-libs/boost-1.52
- dev-python/tabulate
- dev-python/matplotlib
- dev-python/numpy
- sci-libs/scipy
- doc? ( dev-python/sphinx )
+ >=dev-libs/boost-1.52[${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})
@@ -31,25 +31,37 @@ RDEPEND="${DEPEND}"
src_prepare(){
default
- # autogen.sh
- test -n "$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
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2021-01-15 20:28 Andrew Ammerlaan
0 siblings, 0 replies; 12+ messages in thread
From: Andrew Ammerlaan @ 2021-01-15 20:28 UTC (permalink / raw
To: gentoo-commits
commit: 0e4a7cec8abd9f06360d25996f05c7d1633f289d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Jan 15 20:28:03 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Jan 15 20:28:03 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e4a7cec
sci-biology/kat: bump py targets
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kat/kat-2.4.2.ebuild | 15 ++++++++++-----
sci-biology/kat/kat-9999.ebuild | 15 ++++++++++-----
2 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild
index e8f10ad5d..39c4fc6c1 100644
--- a/sci-biology/kat/kat-2.4.2.ebuild
+++ b/sci-biology/kat/kat-2.4.2.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python3_{5,6} )
+PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
inherit flag-o-matic autotools distutils-r1
@@ -23,9 +24,9 @@ CDEPEND="
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]"
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
DEPEND="${CDEPEND}
- dev-python/sphinx
test? ( sys-process/time )"
RDEPEND="${CDEPEND}"
# contains bundled and *modified* version of jellyfish-2.2.0
@@ -40,6 +41,9 @@ PATCHES=(
S="${WORKDIR}"/KAT-Release-"${PV}"
+distutils_enable_sphinx "${S}/doc/source" --no-autodoc
+distutils_enable_tests pytest
+
src_prepare(){
default
rm -rf deps/boost || die "Failed to zap bundled boost"
@@ -75,4 +79,5 @@ src_install(){
src_test(){
default
+ python_foreach_impl python_test
}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 961dc9ce8..752dab83c 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python3_{5,6} )
+PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
# https://github.com/Ensembl/Bio-DB-HTS/issues/30
inherit flag-o-matic autotools distutils-r1 git-r3
@@ -24,9 +25,9 @@ CDEPEND="
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]"
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
DEPEND="${CDEPEND}
- dev-python/sphinx
test? ( sys-process/time )"
RDEPEND="${CDEPEND}"
# contains bundled and *modified* version of jellyfish-2.2.0
@@ -41,6 +42,9 @@ PATCHES=(
S="${WORKDIR}"/KAT-Release-"${PV}"
+distutils_enable_sphinx "${S}/doc/source" --no-autodoc
+distutils_enable_tests pytest
+
src_prepare(){
default
rm -rf deps/boost || die "Failed to zap bundled boost"
@@ -76,4 +80,5 @@ src_install(){
src_test(){
default
+ python_foreach_impl python_test
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/
@ 2021-01-16 9:15 Andrew Ammerlaan
0 siblings, 0 replies; 12+ messages in thread
From: Andrew Ammerlaan @ 2021-01-16 9:15 UTC (permalink / raw
To: gentoo-commits
commit: e37cdb85f0e2b068a5d5c65bbd8a4483d0170b19
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 09:14:59 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 09:14:59 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e37cdb85
sci-biology/kat: remove keywords from live ebuild
oops
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/kat/kat-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 752dab83c..404f0d0c2 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -16,7 +16,7 @@ EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}"
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE="cpu_flags_x86_sse static-libs test"
CDEPEND="
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