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* 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>
* sci-biology/mothur: add github upstream metadataSam James2022-07-301-4/+7
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/fasta: add github upstream metadataSam James2022-07-301-4/+7
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: fix metadata indentationSam James2022-07-301-10/+10
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/bwa: add github upstream metadataSam James2022-07-301-7/+8
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/uchime: update EAPI 7 -> 8David Seifert2022-07-153-28/+26
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/uchime: use append-cxxflagsSam James2022-07-151-2/+2
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/trnascan-se: drop 1.31David Seifert2022-07-092-80/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/trnascan-se: improve makefileDavid Seifert2022-07-093-20/+182
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/rebase: fix RDEPEND typoSam James2022-07-091-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/biopandas: update EAPI 7 -> 8David Seifert2022-07-081-3/+3
| | | | | | Closes: https://bugs.gentoo.org/809665 Closes: https://bugs.gentoo.org/846218 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: update EAPI 7 -> 8David Seifert2022-07-081-6/+5
| | | | | Closes: https://bugs.gentoo.org/846215 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/yass: update EAPI 6 -> 8David Seifert2022-07-071-3/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/trf: update EAPI 6 -> 8David Seifert2022-07-071-8/+7
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/transfac: update EAPI 6 -> 8David Seifert2022-07-071-7/+6
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/t-coffee: update EAPI 6 -> 8David Seifert2022-07-072-17/+29
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/rnaview: update EAPI 6 -> 8David Seifert2022-07-071-8/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/recon: update EAPI 6 -> 8David Seifert2022-07-072-8/+28
| | | | | Closes: https://bugs.gentoo.org/716082 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prodigal: update EAPI 6 -> 8David Seifert2022-07-071-8/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prank: update EAPI 6 -> 8David Seifert2022-07-074-39/+57
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/piler: update EAPI 6 -> 8David Seifert2022-07-071-6/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pilercr: update EAPI 6 -> 8David Seifert2022-07-071-6/+4
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/phyml: update EAPI 6 -> 8David Seifert2022-07-071-8/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/phred: update EAPI 6 -> 8David Seifert2022-07-071-14/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pals: update EAPI 6 -> 8David Seifert2022-07-071-8/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mummer: update EAPI 6 -> 8David Seifert2022-07-071-6/+4
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/maqview: update EAPI 6 -> 8David Seifert2022-07-071-5/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>