[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2023-05-22 Thread Horea Christian 
commit: 5a899bba55649b682d4f3b3ebba06734fb7401e5
Author: Horea Christian  chymera  eu>
AuthorDate: Mon May 22 10:49:14 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon May 22 10:49:14 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5a899bba

sci-biology/gemini: treeclean

Signed-off-by: Horea Christian  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..0
--- 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..0
--- a/sci-biology/gemini/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-   
-   mmokr...@fold.natur.cuni.cz
-   Martin Mokrejs
-   
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-   
-   arq5x/gemini
-   
-

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2023-01-13 Thread Horea Christian 
commit: bf60818f31adf6e848e7d011a620dcd110969772
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Jan 13 19:27:22 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Jan 13 19:27:22 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf60818f

sci-biology/gemini: update EAPI 7 -> 8

Signed-off-by: Horea Christian  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

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2021-01-04 Thread Horea Christian 
commit: 23d1c105b394c8e51de4ef0046c75196a562b62a
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Mon Jan  4 12:41:17 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Jan  5 06:07:59 2021 +
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  riseup.net>
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/gemini/gemini-0.30.2.ebuild | 45 +
 sci-biology/gemini/gemini-.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 0..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-.ebuild 
b/sci-biology/gemini/gemini-.ebuild
deleted file mode 100644
index b6d4ce1af..0
--- a/sci-biology/gemini/gemini-.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

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2017-01-09 Thread Martin Mokrejs 
commit: 19df169a8d18b0af561b32ad346585bdb14b280b
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Jan 10 01:06:22 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 10 01:06:22 2017 +
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-.ebuild | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-biology/gemini/gemini-.ebuild 
b/sci-biology/gemini/gemini-.ebuild
index 7593ec1..6bc7655 100644
--- a/sci-biology/gemini/gemini-.ebuild
+++ b/sci-biology/gemini/gemini-.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!

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2017-01-08 Thread Martin Mokrejs 
commit: dcdce093fe09cd39214280e98f2f2fbee24c5e2c
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Jan  9 01:40:54 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jan  9 01:40:54 2017 +
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-.ebuild | 4 
 1 file changed, 4 insertions(+)

diff --git a/sci-biology/gemini/gemini-.ebuild 
b/sci-biology/gemini/gemini-.ebuild
index f78244a..7593ec1 100644
--- a/sci-biology/gemini/gemini-.ebuild
+++ b/sci-biology/gemini/gemini-.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.

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2017-01-08 Thread Martin Mokrejs 
commit: b2f9c596ad3a27a416963593ac29c65d9c641d3b
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Jan  9 01:20:23 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jan  9 01:20:23 2017 +
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-.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-biology/gemini/gemini-.ebuild 
b/sci-biology/gemini/gemini-.ebuild
index 90cdeaf..f78244a 100644
--- a/sci-biology/gemini/gemini-.ebuild
+++ b/sci-biology/gemini/gemini-.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.
 #

[gentoo-commits] proj/sci:master commit in: sci-biology/gemini/

2016-04-10 Thread Martin Mokrejs 
commit: 83ba99362bb29203a0c28f9174bd68313bf6b5ab
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun Apr 10 19:55:37 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 10 19:55:37 2016 +
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-.ebuild | 29 +
 sci-biology/gemini/metadata.xml   | 12 
 2 files changed, 41 insertions(+)

diff --git a/sci-biology/gemini/gemini-.ebuild 
b/sci-biology/gemini/gemini-.ebuild
new file mode 100644
index 000..90cdeaf
--- /dev/null
+++ b/sci-biology/gemini/gemini-.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 000..f68a1b6
--- /dev/null
+++ b/sci-biology/gemini/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+