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* sci-biology/wgs-assembler: [QA] Pass CC/CXX to build systemDavid Seifert2020-06-212-54/+76
| | | | | | | Closes: https://bugs.gentoo.org/725314 Closes: https://bugs.gentoo.org/725316 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vienna-rna: Remove oldDavid Seifert2020-06-214-149/+0
| | | | | Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/infernal: [QA] Pass AR to build systemDavid Seifert2020-06-215-68/+142
| | | | | | Closes: https://bugs.gentoo.org/725320 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/poa: [QA] Pass AR/RANLIB to build systemDavid Seifert2020-06-212-23/+34
| | | | | | Closes: https://bugs.gentoo.org/725324 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/poa: Fix building against GCC 10David Seifert2020-06-212-0/+14
| | | | | | Closes: https://bugs.gentoo.org/707028 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/abyss: switch from virtual/libffiSergei Trofimovich2020-06-211-1/+1
| | | | | Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/mcl: Fix building against GCC 10David Seifert2020-06-212-5/+31
| | | | | | Closes: https://bugs.gentoo.org/706530 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mcl: [QA] Call AM_PROG_ARDavid Seifert2020-06-212-9/+59
| | | | | | Closes: https://bugs.gentoo.org/725326 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/abyss: drop oldSergei Trofimovich2020-06-213-110/+0
| | | | | Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: disable CFLAGS QA check on samtobreakSergei Trofimovich2020-05-251-0/+8
| | | | | | | | | | | | GHC uses it's own native code generator. Portage's QA check generates false positive because it assumes presence of GCC-specific sections. Workaround false positiove by disabling the check, bug #677600. Bug: https://bugs.gentoo.org/677600 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: respect AR override, bug #725300Sergei Trofimovich2020-05-252-0/+67
| | | | | | | | | | Use AM_PROG_AR to default to standard AR discovery instead of make's 'ar'. Reported-by: Agostino Sarubbo Closes: https://bugs.gentoo.org/725300 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/bioruby: remove masked packageHans de Graaff2020-05-234-54/+0
| | | | Signed-off-by: Hans de Graaff <graaff@gentoo.org>
* sci-biology/clustalx: EAPI-7 bump, update HOMEPAGEAndreas Sturmlechner2020-05-211-4/+4
| | | | | Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/foldingathome: bump to 7.6.13Ian Stakenvicius2020-05-142-1/+1
| | | | | | Closes: https://bugs.gentoo.org/721980 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: Ian Stakenvicius <axs@gentoo.org>
* sci-biology/foldingathome: migrate to eapi7Ian Stakenvicius2020-04-241-3/+3
| | | | | | | includes migration from 'versionator' to 'eapi7-ver' Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: Ian Stakenvicius <axs@gentoo.org>
* sci-biology/foldingathome: version bumpIan Stakenvicius2020-04-242-0/+141
| | | | | | | | Trivial version bump, per bug comments; thanks for testing! Closes: https://bugs.gentoo.org/718584 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: Ian Stakenvicius <axs@gentoo.org>
* sci-biology/mafft: Remove oldDavid Seifert2020-04-224-343/+0
| | | | | Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mafft: Fix -fno-common / GCC 10David Seifert2020-04-222-1/+10
| | | | | | Closes: https://bugs.gentoo.org/707738 Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/kallisto: drop inactive maintainerJoonas Niilola2020-04-141-8/+0
| | | | | Closes: https://bugs.gentoo.org/643652 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/STAR: remove inactive maintainerJoonas Niilola2020-04-141-8/+0
| | | | | Closes: https://bugs.gentoo.org/633132 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/bcftools: remove inactive maintainerJoonas Niilola2020-04-141-4/+0
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/bedtools: remove inactive maintainer & long desc.Joonas Niilola2020-04-141-11/+0
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/bamtools: remove inactive maintainerJoonas Niilola2020-04-141-8/+0
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-biology/HTSeq: remove inactive maintainerJoonas Niilola2020-04-141-8/+0
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* 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>