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* sci-biology/pysam: fix build with cython 3David Seifert2023-04-082-0/+30
| | | | | Closes: https://bugs.gentoo.org/898730 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: drop 1.16David Seifert2023-04-062-43/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: drop 1.16.1David Seifert2023-04-062-48/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: drop 0.20.0David Seifert2023-04-062-70/+0
| | | | | Closes: https://bugs.gentoo.org/836857 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: add 0.21.0David Seifert2023-04-062-0/+67
| | | | | Bug: https://bugs.gentoo.org/836857 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: add 9999David Seifert2023-03-301-0/+72
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.17David Seifert2023-03-302-0/+43
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.17David Seifert2023-03-302-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bowtie: add 2.5.1Andrew Ammerlaan2023-02-242-0/+74
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/biopython: add 1.81Andrew Ammerlaan2023-02-242-0/+62
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/biopandas: add 0.4.1Andrew Ammerlaan2023-02-243-2/+31
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/HTSeq: enable py3.11Andrew Ammerlaan2023-02-243-6/+3
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/bcftools: drop 1.15.1David Seifert2023-02-192-43/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: drop 1.15.1David Seifert2023-02-192-48/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: drop 0.19.1David Seifert2023-02-192-67/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: add 0.20.0David Seifert2023-02-192-0/+70
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: move remote-id inside upstream blockPetr Vaněk2023-02-061-1/+3
| | | | | | | Fixes: f203a8487a2f ("sci-biology/augustus: add github remote-id") Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Closes: https://github.com/gentoo/gentoo/pull/29448 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/augustus: add github remote-idSam James2023-02-041-0/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/augustus: add lpsolve subslot depSam James2023-02-041-2/+2
| | | | | Bug: https://bugs.gentoo.org/614866 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/consed: treecleanJakov Smolić2023-01-277-1688/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/phrap: treecleanJakov Smolić2023-01-274-156/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/phred: treecleanJakov Smolić2023-01-275-173/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* */*: remove py3.8 from PYTHON_COMPATDavid Seifert2023-01-149-18/+18
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.16David Seifert2022-12-272-0/+43
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.16.1David Seifert2022-12-272-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seqan: drop 2.4.0-r1Andreas Sturmlechner2022-12-196-161/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/hmmer: expose XSI pthread_setconcurrency() prototypesDavid Seifert2022-11-201-1/+4
| | | | | Closes: https://bugs.gentoo.org/882279 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/tree-puzzle: regenerate configure script for clang 16David Seifert2022-11-193-15/+368
| | | | | Closes: https://bugs.gentoo.org/879751 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/unafold: fix clang 16 buildDavid Seifert2022-10-233-9/+831
| | | | | Closes: https://bugs.gentoo.org/875041 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/poa: fix clang 16 buildDavid Seifert2022-10-232-1/+76
| | | | | Closes: https://bugs.gentoo.org/875038 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/eugene: fix clang 16 buildDavid Seifert2022-10-232-0/+23
| | | | | Closes: https://bugs.gentoo.org/875476 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/uchime: align longdescription opening and closing tagsPetr Vaněk2022-10-201-9/+9
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/trnascan-se: fix build w/ clang16, pass -std=gnu89Ionen Wolkens2022-10-192-1/+65
| | | | | Closes: https://bugs.gentoo.org/874477 Signed-off-by: Ionen Wolkens <ionen@gentoo.org>
* sci-biology/stride: fix build w/ upcoming clang16Ionen Wolkens2022-10-152-1/+17
| | | | | | | Note that the implicit int is part of the update patch. Closes: https://bugs.gentoo.org/874069 Signed-off-by: Ionen Wolkens <ionen@gentoo.org>
* sci-biology/treeviewx: fix StaticSrcUriSam James2022-10-011-2/+2
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/phred: use PV in SRC_URISam James2022-09-221-1/+1
| | | | | | not that it really matters in this case, but still. Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/express: remove stale boost lower boundsDavid Seifert2022-09-041-2/+2
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: respect CC, CXXSam James2022-09-031-2/+5
| | | | | Closes: https://bugs.gentoo.org/832187 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/augustus: fix Boost depSam James2022-09-031-6/+6
| | | | | Closes: https://bugs.gentoo.org/864773 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/bioperl: use <pkg> tags in metadata.xmlPetr Vaněk2022-08-261-3/+3
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/pals: use HTTPSMichael Mair-Keimberger2022-08-231-2/+2
| | | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Closes: https://github.com/gentoo/gentoo/pull/26708 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/muscle: use HTTPSMichael Mair-Keimberger2022-08-231-3/+3
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/iedera: use HTTPSMichael Mair-Keimberger2022-08-231-3/+3
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/trf: use HTTPSMichael Mair-Keimberger2022-08-231-2/+2
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/biosql: use HTTPSMichael Mair-Keimberger2022-08-231-2/+2
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/exonerate: use HTTPSMichael Mair-Keimberger2022-08-231-1/+1
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Portage 3.0.34 / pkgdev 0.2.1 / pkgcheck 0.10.11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/transfac: treecleanJakov Smolić2022-08-093-59/+0
| | | | | Closes: https://bugs.gentoo.org/361411 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/t-coffee: add github upstream metadataSam James2022-07-301-0/+3
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/newick-utils: add github upstream metadataSam James2022-07-301-0/+3
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/muscle: add github upstream metadataSam James2022-07-301-4/+7
| | | | Signed-off-by: Sam James <sam@gentoo.org>