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
