* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2016-04-10 19:58 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-04-10 19:58 UTC (permalink / raw
To: gentoo-commits
commit: 83ba99362bb29203a0c28f9174bd68313bf6b5ab
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 19:55:37 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 19:55:37 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=83ba9936
sci-biology/gemini: new package
Package-Manager: portage-2.2.28
sci-biology/gemini/gemini-9999.ebuild | 29 +++++++++++++++++++++++++++++
sci-biology/gemini/metadata.xml | 12 ++++++++++++
2 files changed, 41 insertions(+)
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
new file mode 100644
index 0000000..90cdeaf
--- /dev/null
+++ b/sci-biology/gemini/gemini-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=( python2_7 )
+
+inherit git-r3 distutils-r1
+
+DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
+HOMEPAGE="https://github.com/arq5x/gemini
+ http://gemini.readthedocs.org/en/latest"
+EGIT_REPO_URI="https://github.com/arq5x/gemini.git"
+
+LICENSE="MIT" # see note below!
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+# GEMINI includes CADD scores (PMID: 24487276) for annotating variants.
+#
+# CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of
+# Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved)
+# but are freely available for all academic, non-commercial applications.
+# For commercial licensing information contact Jennifer McCullar
diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/gemini/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] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2017-01-09 1:20 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-01-09 1:20 UTC (permalink / raw
To: gentoo-commits
commit: b2f9c596ad3a27a416963593ac29c65d9c641d3b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 9 01:20:23 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 9 01:20:23 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2f9c596
sci-biology/gemini: add missing RDEPEND
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/gemini/gemini-9999.ebuild | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
index 90cdeaf..f78244a 100644
--- a/sci-biology/gemini/gemini-9999.ebuild
+++ b/sci-biology/gemini/gemini-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -19,7 +19,8 @@ KEYWORDS=""
IUSE=""
DEPEND=""
-RDEPEND="${DEPEND}"
+RDEPEND="dev-python/sqlalchemy
+ ${DEPEND}"
# GEMINI includes CADD scores (PMID: 24487276) for annotating variants.
#
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2017-01-09 1:41 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-01-09 1:41 UTC (permalink / raw
To: gentoo-commits
commit: dcdce093fe09cd39214280e98f2f2fbee24c5e2c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 9 01:40:54 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 9 01:40:54 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dcdce093
sci-biology/gemini: more deps needed
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/gemini/gemini-9999.ebuild | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
index f78244a..7593ec1 100644
--- a/sci-biology/gemini/gemini-9999.ebuild
+++ b/sci-biology/gemini/gemini-9999.ebuild
@@ -20,6 +20,10 @@ IUSE=""
DEPEND=""
RDEPEND="dev-python/sqlalchemy
+ sci-biology/grabix
+ sci-libs/htslib
+ sci-biology/bedtools
+ sci-biology/pybedtools
${DEPEND}"
# GEMINI includes CADD scores (PMID: 24487276) for annotating variants.
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2017-01-10 1:06 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-01-10 1:06 UTC (permalink / raw
To: gentoo-commits
commit: 19df169a8d18b0af561b32ad346585bdb14b280b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:06:22 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:06:22 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=19df169a
sci-biology/gemini: add links to existing docs
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/gemini/gemini-9999.ebuild | 3 +++
1 file changed, 3 insertions(+)
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
index 7593ec1..6bc7655 100644
--- a/sci-biology/gemini/gemini-9999.ebuild
+++ b/sci-biology/gemini/gemini-9999.ebuild
@@ -11,6 +11,9 @@ inherit git-r3 distutils-r1
DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
HOMEPAGE="https://github.com/arq5x/gemini
http://gemini.readthedocs.org/en/latest"
+# https://media.readthedocs.org/pdf/gemini/latest/gemini.pdf
+# http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153
+# http://quinlanlab.org/pdf/Gemini-Quinlan-Stroke-UVA.pdf
EGIT_REPO_URI="https://github.com/arq5x/gemini.git"
LICENSE="MIT" # see note below!
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2021-01-05 6:08 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2021-01-05 6:08 UTC (permalink / raw
To: gentoo-commits
commit: 23d1c105b394c8e51de4ef0046c75196a562b62a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 4 12:41:17 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan 5 06:07:59 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=23d1c105
sci-biology/gemini: bump py targets, add keywords
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/gemini/gemini-0.30.2.ebuild | 45 +++++++++++++++++++++++++++++++++
sci-biology/gemini/gemini-9999.ebuild | 36 --------------------------
2 files changed, 45 insertions(+), 36 deletions(-)
diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild
new file mode 100644
index 000000000..f041c2c48
--- /dev/null
+++ b/sci-biology/gemini/gemini-0.30.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
+HOMEPAGE="https://github.com/arq5x/gemini
+ http://gemini.readthedocs.org/en/latest"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/bottle[${PYTHON_USEDEP}]
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/ipyparallel[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/numexpr[${PYTHON_USEDEP}]
+ dev-python/openpyxl[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/unidecode[${PYTHON_USEDEP}]
+ dev-python/sqlalchemy[${PYTHON_USEDEP}]
+ sci-biology/bx-python[${PYTHON_USEDEP}]
+ sci-libs/htslib
+ sci-biology/pybedtools[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]
+"
+
+distutils_enable_sphinx docs
+
+python_prepare_all() {
+ # this has been renamed in newer versions of sphinx
+ sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die
+
+ distutils-r1_python_prepare_all
+}
diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild
deleted file mode 100644
index b6d4ce1af..000000000
--- a/sci-biology/gemini/gemini-9999.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit git-r3 distutils-r1
-
-DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
-HOMEPAGE="https://github.com/arq5x/gemini
- http://gemini.readthedocs.org/en/latest"
-# https://media.readthedocs.org/pdf/gemini/latest/gemini.pdf
-# http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153
-# http://quinlanlab.org/pdf/Gemini-Quinlan-Stroke-UVA.pdf
-EGIT_REPO_URI="https://github.com/arq5x/gemini.git"
-
-LICENSE="MIT" # see note below!
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="dev-python/sqlalchemy
- sci-biology/grabix
- sci-libs/htslib
- sci-biology/bedtools
- sci-biology/pybedtools
- ${DEPEND}"
-
-# GEMINI includes CADD scores (PMID: 24487276) for annotating variants.
-#
-# CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of
-# Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved)
-# but are freely available for all academic, non-commercial applications.
-# For commercial licensing information contact Jennifer McCullar
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2023-01-13 19:27 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2023-01-13 19:27 UTC (permalink / raw
To: gentoo-commits
commit: bf60818f31adf6e848e7d011a620dcd110969772
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 19:27:22 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 19:27:22 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf60818f
sci-biology/gemini: update EAPI 7 -> 8
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/gemini/gemini-0.30.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild
index f041c2c48..25ec22946 100644
--- a/sci-biology/gemini/gemini-0.30.2.ebuild
+++ b/sci-biology/gemini/gemini-0.30.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/
@ 2023-05-22 10:53 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2023-05-22 10:53 UTC (permalink / raw
To: gentoo-commits
commit: 5a899bba55649b682d4f3b3ebba06734fb7401e5
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon May 22 10:49:14 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon May 22 10:49:14 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5a899bba
sci-biology/gemini: treeclean
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/gemini/gemini-0.30.2.ebuild | 45 ---------------------------------
sci-biology/gemini/metadata.xml | 15 -----------
2 files changed, 60 deletions(-)
diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild
deleted file mode 100644
index 25ec22946..000000000
--- a/sci-biology/gemini/gemini-0.30.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..10} )
-
-inherit distutils-r1
-
-DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics"
-HOMEPAGE="https://github.com/arq5x/gemini
- http://gemini.readthedocs.org/en/latest"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/bottle[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/ipyparallel[${PYTHON_USEDEP}]
- dev-python/jinja[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/numexpr[${PYTHON_USEDEP}]
- dev-python/openpyxl[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/unidecode[${PYTHON_USEDEP}]
- dev-python/sqlalchemy[${PYTHON_USEDEP}]
- sci-biology/bx-python[${PYTHON_USEDEP}]
- sci-libs/htslib
- sci-biology/pybedtools[${PYTHON_USEDEP}]
- sci-biology/pysam[${PYTHON_USEDEP}]
-"
-
-distutils_enable_sphinx docs
-
-python_prepare_all() {
- # this has been renamed in newer versions of sphinx
- sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die
-
- distutils-r1_python_prepare_all
-}
diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml
deleted file mode 100644
index 260a8b4ae..000000000
--- a/sci-biology/gemini/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="github">arq5x/gemini</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
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