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* sci-biology/biopython: Remove old 1.73David Seifert2020-08-222-58/+0
| | | | | Package-Manager: Portage-3.0.4, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopython: Version bump to 1.77David Seifert2020-08-222-0/+63
| | | | | Package-Manager: Portage-3.0.4, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopandas: Remove old 0.2.1David Seifert2020-08-172-44/+0
| | | | | | Closes: https://bugs.gentoo.org/718470 Package-Manager: Portage-3.0.3, Repoman-3.0.0 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopandas: Version bump to 0.2.7David Seifert2020-08-172-0/+41
| | | | | | Bug: https://bugs.gentoo.org/718470 Package-Manager: Portage-3.0.3, Repoman-3.0.0 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Add missing ${PYTHON_DEPS} to BDEPENDDavid Seifert2020-08-161-1/+3
| | | | | Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Remove oldDavid Seifert2020-08-162-46/+0
| | | | | | Closes: https://bugs.gentoo.org/718468 Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Version bump to 2.29.2David Seifert2020-08-165-0/+185
| | | | | | Bug: https://bugs.gentoo.org/718468 Package-Manager: Portage-3.0.2, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: Remove oldDavid Seifert2020-08-034-525/+0
| | | | | | Closes: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: Remove oldDavid Seifert2020-08-037-148/+0
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: Remove oldDavid Seifert2020-08-033-111/+0
| | | | | | | | Closes: https://bugs.gentoo.org/645060 Closes: https://bugs.gentoo.org/646986 Closes: https://bugs.gentoo.org/718472 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: [QA] Fix UnnecessarySlashStripDavid Seifert2020-08-031-5/+5
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: Remove ancient py2 varfilter.py scriptDavid Seifert2020-08-031-23/+13
| | | | | | Closes: https://bugs.gentoo.org/735444 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Remove oldDavid Seifert2020-08-032-32/+0
| | | | | | | | | * Remove the package.mask entry again Closes: https://bugs.gentoo.org/696484 Closes: https://bugs.gentoo.org/718466 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Sync live ebuildDavid Seifert2020-08-031-6/+8
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: Bump to 0.12.4David Seifert2020-08-032-0/+34
| | | | | | | Bug: https://bugs.gentoo.org/696484 Bug: https://bugs.gentoo.org/718466 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: Bump to 0.16.0.1David Seifert2020-08-033-0/+98
| | | | | | | | Bug: https://bugs.gentoo.org/645060 Bug: https://bugs.gentoo.org/646986 Bug: https://bugs.gentoo.org/718472 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: Bump to version 1.10.2David Seifert2020-08-032-0/+44
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: Bump to version 1.10David Seifert2020-08-032-0/+57
| | | | | | Bug: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/clustalw: keyworded 2.1-r1 for sparcSergei Trofimovich2020-07-191-1/+1
| | | | | | | | keyworded wrt bug #732334 Package-Manager: Portage-2.3.103, Repoman-2.3.23 RepoMan-Options: --include-arches="sparc" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/clustalw: ppc keyworded (bug #732334)Sam James2020-07-171-1/+1
| | | | | Package-Manager: Portage-2.3.103, Repoman-2.3.23 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/clustalw: keyworded 2.1-r1 for ppc64Sergei Trofimovich2020-07-121-2/+2
| | | | | | | | keyworded wrt bug #732334 Package-Manager: Portage-2.3.103, Repoman-2.3.23 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/blat: -fno-common fixDavid Denoncin2020-07-042-2/+16
| | | | | | | | Closes: https://bugs.gentoo.org/706450 Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: David Denoncin <ddenoncin@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/16587 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* */*: drop last-rited py2 packagesAaron Bauman2020-07-035-227/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* 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>