From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 149101382C5 for ; Tue, 5 Jan 2021 06:08:15 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B7DCBE0827; Tue, 5 Jan 2021 06:08:13 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 1FD54E07FE for ; Tue, 5 Jan 2021 06:08:13 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 3832E33BF35 for ; Tue, 5 Jan 2021 06:08:11 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B1F0346B for ; Tue, 5 Jan 2021 06:08:09 +0000 (UTC) From: "Horea Christian" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" Message-ID: <1609826879.23d1c105b394c8e51de4ef0046c75196a562b62a.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gemini/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gemini/gemini-0.30.2.ebuild sci-biology/gemini/gemini-9999.ebuild X-VCS-Directories: sci-biology/gemini/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 23d1c105b394c8e51de4ef0046c75196a562b62a X-VCS-Branch: master Date: Tue, 5 Jan 2021 06:08:09 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 0cddb170-bf38-4596-ae44-2c8f15b47c32 X-Archives-Hash: 21d1229fce519937a91d03910e88399a commit: 23d1c105b394c8e51de4ef0046c75196a562b62a Author: Andrew Ammerlaan riseup net> AuthorDate: Mon Jan 4 12:41:17 2021 +0000 Commit: Horea Christian gmail 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 riseup.net> Signed-off-by: Horea Christian 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