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