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* sci-biology/tree-puzzle: fix build system and MPIDavid Seifert2022-01-292-12/+375
| | | | | | | Closes: https://bugs.gentoo.org/690900 Closes: https://bugs.gentoo.org/810502 Closes: https://bugs.gentoo.org/814185 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: add forgotten runtime dependencyAndrew Ammerlaan2022-01-281-0/+1
| | | | | | Closes: https://bugs.gentoo.org/832186 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/augustus: add version 3.4.0Andrew Ammerlaan2022-01-272-0/+48
| | | | | | Closes: https://bugs.gentoo.org/515996 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/mrbayes: add version 3.2.7Andrew Ammerlaan2022-01-273-9/+56
| | | | | | Closes: https://bugs.gentoo.org/521510 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/gibbs: treecleanJakov Smolić2022-01-164-72/+0
| | | | | Bug: https://bugs.gentoo.org/829216 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/abyss: drop version 2.0.3Andrew Ammerlaan2022-01-133-76/+0
| | | | | | | Closes: https://bugs.gentoo.org/741154 Closes: https://bugs.gentoo.org/715718 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/abyss: add version 2.3.4Andrew Ammerlaan2022-01-132-0/+58
| | | | | | Closes: https://bugs.gentoo.org/646478 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/picard: treecleanJakov Smolić2022-01-084-212/+0
| | | | | | | Closes: https://bugs.gentoo.org/776298 Closes: https://bugs.gentoo.org/580176 Closes: https://bugs.gentoo.org/572142 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/biopython: drop 1.77David Seifert2021-12-302-62/+0
| | | | | | Closes: https://bugs.gentoo.org/757867 Closes: https://bugs.gentoo.org/780345 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/ApE: treecleanJakov Smolić2021-12-263-59/+0
| | | | | Closes: https://bugs.gentoo.org/827522 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/biopython: add 1.79David Seifert2021-12-202-0/+63
| | | | | | Bug: https://bugs.gentoo.org/757867 Bug: https://bugs.gentoo.org/780345 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/ApE: update HOMEPAGE, SRC_URI; s/eutils/desktop/Marek Szuba2021-11-261-4/+4
| | | | | Closes: https://bugs.gentoo.org/809065 Signed-off-by: Marek Szuba <marecki@gentoo.org>
* sci-biology/stride: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-1/+1
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-biology/muscle: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-biology/phyml: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-biology/clustalw: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-biology/samtools: drop 1.10-r1David Seifert2021-10-112-57/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: drop 1.10.2David Seifert2021-10-112-44/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: drop 0.16.0.1-r1David Seifert2021-10-113-98/+0
| | | | | Closes: https://bugs.gentoo.org/812242 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: block <setuptools-58 for 0.16.0.1Arthur Zamarin2021-10-091-4/+4
| | | | | | | Was fixed for 0.17.0 Bug: https://bugs.gentoo.org/812242 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-biology/pysam: add 0.17.0David Seifert2021-10-032-0/+67
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.13David Seifert2021-10-032-0/+45
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.13David Seifert2021-10-032-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mira: Remove last-rited packageJakov Smolić2021-09-286-173/+0
| | | | | | | Closes: https://bugs.gentoo.org/808667 Closes: https://bugs.gentoo.org/585942 Closes: https://bugs.gentoo.org/731880 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* **/metadata.xml: Replace http by https in DOCTYPE elementUlrich Müller2021-09-11129-129/+129
| | | | | Bug: https://bugs.gentoo.org/552720 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/wgs-assembler: Remove last-rited packageJakov Smolić2021-09-045-351/+0
| | | | | | | | Closes: https://bugs.gentoo.org/610094 Closes: https://bugs.gentoo.org/715874 Closes: https://bugs.gentoo.org/731860 Closes: https://bugs.gentoo.org/739486 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/ncbi-tools: Remove last-rited packageJakov Smolić2021-08-3010-546/+0
| | | | | | | | | | | | Closes: https://bugs.gentoo.org/649930 Closes: https://bugs.gentoo.org/782790 Closes: https://bugs.gentoo.org/741188 Closes: https://bugs.gentoo.org/715636 Closes: https://bugs.gentoo.org/710338 Closes: https://bugs.gentoo.org/701340 Closes: https://bugs.gentoo.org/586982 Closes: https://bugs.gentoo.org/295584 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/njplot: Remove last-rited packageJakov Smolić2021-08-305-129/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/psipred: Remove last-rited packageJakov Smolić2021-08-306-155/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/wise: Port to EAPI 8Jakov Smolic2021-08-223-73/+109
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mrbayes: Port to EAPI 8Jakov Smolic2021-08-222-22/+13
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/plink: Port to EAPI 8Jakov Smolic2021-08-221-6/+7
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/velvet: Port to EAPI 8Jakov Smolic2021-08-221-9/+6
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bioperl-db: Drop 1.6.9 (r0), EAPI5--Andreas Sturmlechner2021-08-191-47/+0
| | | | | | Closes: https://bugs.gentoo.org/808198 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/bioperl-db: x86 stable wrt bug #808198Agostino Sarubbo2021-08-191-1/+1
| | | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.2 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bioperl-db: amd64 stable wrt bug #808198Agostino Sarubbo2021-08-161-1/+1
| | | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.2 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/embassy-vienna: remove `append-cflags -std=gnu89`David Seifert2021-08-022-7/+37
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/emboss: Fix C99 `bool` clashDavid Seifert2021-08-016-562/+10
| | | | | | | * Also fix `-Wimplicit-function-declaration` Closes: https://bugs.gentoo.org/695380 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bowtie: fix QA issuesDavid Seifert2021-08-012-13/+8
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bowtie: drop 2.2.9David Seifert2021-08-013-91/+0
| | | | | Closes: https://bugs.gentoo.org/722870 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bowtie: add 2.4.4David Seifert2021-08-012-0/+56
| | | | | Bug: https://bugs.gentoo.org/722870 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mosaik: Fix GCC 11 buildDavid Seifert2021-07-262-4/+64
| | | | | Closes: https://bugs.gentoo.org/788331 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/abyss: drop haskell@ from maintainersSergei Trofimovich2021-07-241-4/+0
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/foldingathome: drop old versionConrad Kostecki2021-07-181-140/+0
| | | | | | Closes: https://bugs.gentoo.org/781485 Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Conrad Kostecki <conikost@gentoo.org>
* sci-biology/foldingathome: migrate to GLEP 81Conrad Kostecki2021-07-181-0/+138
| | | | | | Bug: https://bugs.gentoo.org/781485 Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Conrad Kostecki <conikost@gentoo.org>
* sci-biology/samtools: Add sys-libs/ncurses[unicode(+)]David Seifert2021-07-171-2/+2
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: PYTHON_MULTI_USEDEP -> PYTHON_USEDEPDavid Seifert2021-07-171-3/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bamtools: drop 2.5.1David Seifert2021-06-202-34/+0
| | | | | Closes: https://bugs.gentoo.org/787200 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bamtools: add 2.5.2David Seifert2021-06-202-0/+34
| | | | | Bug: https://bugs.gentoo.org/787200 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/plink: include DEPEND in RDEPENDSam James2021-06-181-4/+6
| | | | | Signed-off-by: Sam James <sam@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>