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* 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>
* sci-biology/ncbi-tools: add pkgconfig or pkgconfig-referenced libs depsSam James2021-06-181-0/+2
| | | | | | | | | | Add dependencies for either virtual/pkgconfig, move it into BDEPEND where applicable, or add dependencies for libraries we're trying to find with pkgconfig. Package-Manager: Portage-3.0.18-prefix, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mira: Depend on dev-libs/boost:=[threads(+)]David Seifert2021-06-181-1/+1
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/uchime: workaround failure with GCC 11Sam James2021-06-151-2/+9
| | | | | | | | Force C++14 for now because we don't really want a large patch for typedefs. Closes: https://bugs.gentoo.org/786297 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ucsc-genome-browser: fix VariableScope ((E)ROOT)Sam James2021-06-111-4/+6
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/amap: Support newer javaPacho Ramos2021-06-061-4/+4
| | | | | | | | | And fix homepage Closes: https://bugs.gentoo.org/787641 Closes: https://bugs.gentoo.org/626674 Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-biology/GBrowse: fix BadDefaultUseFlagsSam James2021-06-031-2/+2
| | | | | | | | | | | -foo in IUSE is discouraged. It is equivalent (in every meaningful case) to 'foo' but confuses parsing tools like e.g. packages.gentoo.org. Dropping '-' from these flags has no impact on the actual default behaviour. See: https://devmanual.gentoo.org/general-concepts/use-flags/index.html#iuse-defaults Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/bioperl-run: fix BadDefaultUseFlagsSam James2021-06-031-2/+2
| | | | | | | | | | | -foo in IUSE is discouraged. It is equivalent (in every meaningful case) to 'foo' but confuses parsing tools like e.g. packages.gentoo.org. Dropping '-' from these flags has no impact on the actual default behaviour. See: https://devmanual.gentoo.org/general-concepts/use-flags/index.html#iuse-defaults Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/embassy-mse: ncurses isn't optionalDavid Seifert2021-05-162-10/+10
| | | | | | Closes: https://bugs.gentoo.org/790515 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add missing multilib inherit for get_libnameSam James2021-05-131-2/+2
| | | | | | | | Found using: `grep -rsn -L -e "inherit.*multilib.*" | xargs grep "get_libname"` Signed-off-by: Sam James <sam@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/treeviewx: Respect ARDavid Seifert2021-05-092-0/+11
| | | | | | Closes: https://bugs.gentoo.org/780456 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/kallisto: Remove live ebuildDavid Seifert2021-05-081-25/+0
| | | | | | | * Upstream is barely active and doesn't merge PRs Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/kallisto: Remove old 0.43.1David Seifert2021-05-082-26/+0
| | | | | | | | Closes: https://bugs.gentoo.org/696504 Closes: https://bugs.gentoo.org/708658 Closes: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/kallisto: Bump to 0.46.2David Seifert2021-05-086-0/+325
| | | | | | | | Bug: https://bugs.gentoo.org/696504 Bug: https://bugs.gentoo.org/708658 Bug: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gatk: Remove last-rited pkgJakov Smolic2021-05-043-44/+0
| | | | | | | | | | | | Closes: https://bugs.gentoo.org/780396 Closes: https://bugs.gentoo.org/574632 Closes: https://bugs.gentoo.org/542940 Closes: https://bugs.gentoo.org/515816 Closes: https://bugs.gentoo.org/431644 Closes: https://bugs.gentoo.org/418625 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Closes: https://github.com/gentoo/gentoo/pull/20667 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/diya: Remove last-rited pkgJakov Smolic2021-05-043-54/+0
| | | | | | Closes: https://bugs.gentoo.org/625492 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/stride: Re-host distfilesPacho Ramos2021-05-021-1/+1
| | | | | | | Thanks-to: Martin Mokrejš Closes: https://bugs.gentoo.org/689774 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>