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* sci-biology/foldingathome: revbump due to RDEPEND changeJoonas Niilola2020-03-281-0/+0
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/foldingathome: systemd cleanup, various fixes.Brian Harring2020-03-281-7/+13
| | | | | | | | | | | | | | | | | | | | 1) force the `foldingathome` user group for the process for obvious reasons. 2) link in the video group and add it to the foldingathome user- this is necessary for GPU utilization. 3) force nice=19 from systemd level. The batch processing attempts to do this for workers, but we might as well force it for the scheduler. 4) Add explicit configuration directives to force- irregardless of host config- the scheduler to be foreground'd and running in a fashion that integrates w/ systemd more sanely. 5) Lockdown some basic systemd security while I'm in here. 6) Finally, drop the pidfile directive for systemd. Foreground process- no pidfile to track (nor should we have the unit create it). Bug: https://bugs.gentoo.org/712744 Signed-off-by: Brian Harring <ferringb@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/15145 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/foldingathome: revert init fixJoonas Niilola2020-03-271-2/+2
| | | | | | | | - apparently it broke for some users, needs more testing and feedback. Bug: https://bugs.gentoo.org/714160 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/samtools: Remove python dependencyDavid Seifert2020-03-271-11/+8
| | | | | | Closes: https://bugs.gentoo.org/710252 Package-Manager: Portage-2.3.96, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: Add python 3.7David Seifert2020-03-271-1/+1
| | | | | Package-Manager: Portage-2.3.96, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/foldingathome: attempt to fix init and service filesJoonas Niilola2020-03-271-4/+4
| | | | | | | | - non-maintainer commit, since axs seems to be inactive. Bug: https://bugs.gentoo.org/712744 Bug: https://bugs.gentoo.org/714160 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/clustalw: Drop alpha keywordsMatt Turner2020-03-151-1/+1
| | | | Signed-off-by: Matt Turner <mattst88@gentoo.org>
* sci-biology/foldingathome: add enewgroupIan Stakenvicius2020-03-041-1/+2
| | | | | | Closes: https://bugs.gentoo.org/711418 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Ian Stakenvicius <axs@gentoo.org>
* sci-biology/tophat: remove last-rited packageMikle Kolyada2020-02-286-310/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* sci-biology/qrna: Port to EAPI 7David Seifert2020-02-232-14/+358
| | | | | | Closes: https://bugs.gentoo.org/710554 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/tophat: [QA] inherit eutils.eclass directlyDavid Seifert2020-02-161-1/+1
| | | | | Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/poa: [QA] inherit toolchain-funcs.eclass directlyDavid Seifert2020-02-131-2/+2
| | | | | Package-Manager: Portage-2.3.88, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: Bump copyright on files touched this yearMichał Górny2020-02-111-1/+1
| | | | | | | Update the copyright notice on all files that were touched since January 1st but did not have the notice updated. Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/pysam: Remove py2Michał Górny2020-02-111-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bedtools: Remove py2 where possibleMichał Górny2020-02-101-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/tophat: Switch to PYTHON_MULTI_USEDEP APIMichał Górny2020-02-091-3/+5
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bcftools: Switch to PYTHON_MULTI_USEDEP APIMichał Górny2020-02-091-1/+3
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bcftools: fix PYTHON_COMPAT, add missing matplotlib depMartin Mokrejs2020-02-072-4/+14
| | | | | | | | | | | | From NEWS one can infer bcftools was at least from about 1.7 version python3 compatible. Moreover, at the moment the shenbang lines specifically call python3.6. So, adjust the PYTHON_COMPAT accordingly. matplotlib is used by the python scripts, unconditionally. Package-Manager: Portage-2.3.84, Repoman-2.3.20 Closes: https://github.com/gentoo/gentoo/pull/14421 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> Signed-off-by: David Seifert <soap@gentoo.org>
* */*: Drop stable alpha keywordsMatt Turner2020-01-251-1/+1
| | | | Signed-off-by: Matt Turner <mattst88@gentoo.org>
* sci-biology/bwa: Fix -fno-common bugDavid Seifert2020-01-252-4/+13
| | | | | | Closes: https://bugs.gentoo.org/706348 Package-Manager: Portage-2.3.85, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Remove Python 2Michał Górny2020-01-162-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/biopandas: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Switch sci-biology proj to cmake.eclassAndreas Sturmlechner2020-01-052-6/+6
| | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* */*: Clean PYTHON_COMPAT of obsolete implsMichał Górny2020-01-056-12/+12
| | | | | Closes: https://github.com/gentoo/gentoo/pull/14246 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/biopython: Drop python2_7Andreas Sturmlechner2019-12-291-2/+1
| | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/biopython: Remove oldDavid Seifert2019-12-293-114/+0
| | | | | Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Change LICENSE to "free-noncomm".Ulrich Müller2019-12-281-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702534 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/phylip: Change LICENSE to "free-noncomm".Ulrich Müller2019-12-281-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702536 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/embassy: Fix LICENSE.Ulrich Müller2019-12-241-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702532 Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/gatk: Drop broken -9999Michał Górny2019-12-151-40/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-run: Drop unmaintained -9999Michał Górny2019-12-151-40/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-network: Drop unmaintained -9999Michał Górny2019-12-151-31/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-db: Drop unmaintained -9999Michał Górny2019-12-151-37/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl: Drop unmaintained -9999Michał Górny2019-12-151-73/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: [QA] Remove redundant `|| die` guardsDavid Seifert2019-12-116-9/+9
| | | | | | | | | | | | * Since all ebuilds in the tree are EAPI>=4, `|| die` on builtin commands is redundant and dead code. Closes: https://github.com/gentoo/gentoo/pull/13940 Reviewed-by: Ulrich Müller <ulm@gentoo.org> Reviewed-by: Michał Górny <mgorny@gentoo.org> Reviewed-by: Andreas K. Hüttel <dilfridge@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/shrimp: Remove oldDavid Seifert2019-12-112-55/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/velvet: Port to EAPI 7David Seifert2019-12-113-126/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: Port to EAPI 7David Seifert2019-12-111-9/+10
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/tree-puzzle: Port to EAPI 7David Seifert2019-12-111-21/+18
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mrbayes: Remove oldDavid Seifert2019-12-111-51/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/plink: Remove oldDavid Seifert2019-12-115-164/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/last: Remove oldDavid Seifert2019-12-112-40/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gibbs: Port to EAPI 7David Seifert2019-12-112-18/+27
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/glimmerhmm: Port to EAPI 7David Seifert2019-12-112-17/+34
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: [QA] Fix trivial cases of MissingTestRestrictMichał Górny2019-12-1113-11/+24
| | | | | | | | | | | | | | | | | | The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/mcl: drop old EAPIAaron Bauman2019-11-233-74/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/psipred: drop old EAPIAaron Bauman2019-11-233-107/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/ariadne: drop last-rited packageAaron Bauman2019-11-205-100/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/bamtools: Remove USE="static-libs"David Seifert2019-11-132-60/+6
| | | | | Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/goby-cpp: Remove last-rited pkgMichał Górny2019-10-145-104/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>