* [gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
@ 2018-01-29 15:29 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-29 15:29 UTC (permalink / raw
To: gentoo-commits
commit: 1a1e9755d0985ab7f3e9107be9125aead76d1b7c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 29 15:29:09 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 29 15:29:09 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a1e9755
sci-biology/chiron: new package
Will need more work to get CPU- and GPU-based features enabled
at once, or will need two separate installs?
Package-Manager: Portage-2.3.20, Repoman-2.3.6
sci-biology/chiron/chiron-9999.ebuild | 22 ++++++++++++++++++++++
sci-biology/chiron/metadata.xml | 12 ++++++++++++
2 files changed, 34 insertions(+)
diff --git a/sci-biology/chiron/chiron-9999.ebuild b/sci-biology/chiron/chiron-9999.ebuild
new file mode 100644
index 000000000..daf1c15b9
--- /dev/null
+++ b/sci-biology/chiron/chiron-9999.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 pypy )
+
+inherit distutils-r1 eutils git-r3
+
+DESCRIPTION="Basecaller for OxfordNanopore data using deep learning"
+HOMEPAGE="https://github.com/haotianteng/chiron
+ https://www.biorxiv.org/content/early/2017/09/12/179531"
+EGIT_REPO_URI="https://github.com/haotianteng/chiron"
+
+LICENSE="MPL-2.0"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-python/h5py"
diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/chiron/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
@ 2018-01-29 15:31 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-29 15:31 UTC (permalink / raw
To: gentoo-commits
commit: a12f311c601712550558fc506c30231f21c07a7d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 29 15:31:54 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 29 15:31:54 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12f311c
sci-biology/chiron: add the dependency on =sci-libs/tensorflow-1.0.1
Seems tensorflow so changing a lot and versions are really incompatible
with each other.
Package-Manager: Portage-2.3.20, Repoman-2.3.6
sci-biology/chiron/chiron-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/chiron/chiron-9999.ebuild b/sci-biology/chiron/chiron-9999.ebuild
index daf1c15b9..cd99cb976 100644
--- a/sci-biology/chiron/chiron-9999.ebuild
+++ b/sci-biology/chiron/chiron-9999.ebuild
@@ -17,6 +17,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="=sci-libs/tensorflow-1.0.1"
RDEPEND="${DEPEND}
dev-python/h5py"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
@ 2019-04-13 20:36 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2019-04-13 20:36 UTC (permalink / raw
To: gentoo-commits
commit: e5ce549c694e952e624f1c4b2b751db1618294ec
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 13 20:36:02 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 13 20:36:02 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5ce549c
sci-biology/chiron: Fix RDEPEND issue
RDEPEND uses the = operator with no revision:
'=sci-libs/tensorflow-1.0.1';
if any revision is acceptable, use '~' instead;
if only -r0 then please append '-r0' to the dep
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/chiron/chiron-9999.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/chiron/chiron-9999.ebuild b/sci-biology/chiron/chiron-9999.ebuild
index cd99cb976..4294326ee 100644
--- a/sci-biology/chiron/chiron-9999.ebuild
+++ b/sci-biology/chiron/chiron-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 pypy )
@@ -17,6 +17,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="=sci-libs/tensorflow-1.0.1"
+DEPEND="~sci-libs/tensorflow-1.0.1"
RDEPEND="${DEPEND}
dev-python/h5py"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
@ 2021-01-05 18:05 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:05 UTC (permalink / raw
To: gentoo-commits
commit: 5c00b7d3b2bf6c5febb225a4abf08960ca83f42d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 15:53:08 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:05:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c00b7d3
sci-biology/chiron: bump py targets, add keywords
Closes: https://github.com/gentoo/sci/pull/1037
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/chiron/chiron-0.6.1.1.ebuild | 29 +++++++++++++++++++++++++++++
sci-biology/chiron/chiron-9999.ebuild | 22 ----------------------
2 files changed, 29 insertions(+), 22 deletions(-)
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild
new file mode 100644
index 000000000..645e4ed30
--- /dev/null
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="A deep neural network basecaller for nanopore sequencing"
+HOMEPAGE="https://github.com/haotianteng/chiron
+ https://www.biorxiv.org/content/early/2017/09/12/179531"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ sci-biology/mappy[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ sci-biology/biopython[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ sci-libs/tensorflow[${PYTHON_USEDEP}]
+"
diff --git a/sci-biology/chiron/chiron-9999.ebuild b/sci-biology/chiron/chiron-9999.ebuild
deleted file mode 100644
index 4294326ee..000000000
--- a/sci-biology/chiron/chiron-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 pypy )
-
-inherit distutils-r1 eutils git-r3
-
-DESCRIPTION="Basecaller for OxfordNanopore data using deep learning"
-HOMEPAGE="https://github.com/haotianteng/chiron
- https://www.biorxiv.org/content/early/2017/09/12/179531"
-EGIT_REPO_URI="https://github.com/haotianteng/chiron"
-
-LICENSE="MPL-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="~sci-libs/tensorflow-1.0.1"
-RDEPEND="${DEPEND}
- dev-python/h5py"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
@ 2022-01-26 17:48 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-26 17:48 UTC (permalink / raw
To: gentoo-commits
commit: 8c097d1bb613ea66723b7088712299d54f3e32c0
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 26 16:27:00 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jan 26 16:27:00 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c097d1b
sci-biology/chiron: bump python compat
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/chiron/chiron-0.6.1.1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild
index 645e4ed30..162a03129 100644
--- a/sci-biology/chiron/chiron-0.6.1.1.ebuild
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
^ permalink raw reply related [flat|nested] 5+ messages in thread
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