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* sci-biology/embassy-clustalomega: Port to EAPI 7David Seifert2021-03-131-2/+2
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-clustalomega: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731754 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-esim4: Port to EAPI 7David Seifert2021-03-131-2/+2
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-esim4: Fix building against clang/LLDDavid Seifert2021-03-131-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731742 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domsearch: Port to EAPI 7David Seifert2021-03-131-2/+2
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domsearch: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731740 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-mse: EAPI-7 bumpAndreas Sturmlechner2021-03-121-3/+3
| | | | | | Bug: https://bugs.gentoo.org/770262 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/emboss: EAPI-7 bump, minor styleAndreas Sturmlechner2021-03-121-9/+8
| | | | | | Bug: https://bugs.gentoo.org/770262 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/express: EAPI-7/cmake.eclass, new HOMEPAGE/SRC_URIAndreas Sturmlechner2021-03-071-6/+6
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/seqan: Drop 2.4.0 (r0)Andreas Sturmlechner2021-03-071-76/+0
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/seqan: Drop unmaintained live ebuildAndreas Sturmlechner2021-03-071-81/+0
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/seqan: Port to EAPI-7, cmake.eclass, httpsAndreas Sturmlechner2021-03-074-17/+151
| | | | | | | | | | - Fix cmake config install path - Fix pkgconfig install path - Fix examples install path - Fix build with BUILD_SHARED_LIBS=ON default Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/uchime: EAPI-7 bump, use cmake.eclass, https, fix HOMEPAGEAndreas Sturmlechner2021-03-072-12/+11
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/fasttree: Drop 2.1.8Andreas Sturmlechner2021-03-073-75/+0
| | | | | Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/fasttree: 2.1.11 version bump, EAPI-7, cmake.eclassAndreas Sturmlechner2021-03-074-12/+84
| | | | | | Closes: https://bugs.gentoo.org/594364 Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/phylip: remove whitespaceMichael Mair-Keimberger2021-03-051-2/+2
| | | | | | | Package-Manager: Portage-3.0.15, Repoman-3.0.2 Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Closes: https://github.com/gentoo/gentoo/pull/19778 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ucsc-genome-browser: add gcc 10 workaroundSam James2021-03-031-1/+6
| | | | | Closes: https://bugs.gentoo.org/708064 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/finchtv: Remove oldJakov Smolic2021-02-271-29/+0
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/finchtv: Stabilize 1.3.1-r3 amd64, #770757Sam James2021-02-271-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/finchtv: x86 stable wrt bug #770757Agostino Sarubbo2021-02-261-1/+1
| | | | | | Package-Manager: Portage-3.0.13, Repoman-3.0.2 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bedtools: bump to 2.30.0Wolfgang E. Sanyer2021-02-232-0/+50
| | | | | | | | | | * The samtools patch is no longer needed, as upstream has fixed this. Test suite passes without it now. Closes: https://github.com/gentoo/gentoo/pull/19616 Closes: https://bugs.gentoo.org/696188 Signed-off-by: Wolfgang E. Sanyer <ezzieyguywuf@gmail.com> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/finchtv: Port to EAPI 7Jakov Smolic2021-02-171-8/+9
| | | | | | | Closes: https://bugs.gentoo.org/731914 Bug: https://bugs.gentoo.org/770757 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* */*: Remove obsolete values from PYTHON_COMPATMichał Górny2021-01-317-7/+7
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/rebase: Remove oldJakov Smolic2021-01-188-322/+0
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/psipred: Remove oldJakov Smolic2021-01-182-57/+0
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/foldingathome: Remove oldJakov Smolic2021-01-182-141/+0
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/stride: drop x86-macosFabian Groffen2021-01-061-2/+2
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
* sci-biology/mira: drop x86-macosFabian Groffen2021-01-061-2/+2
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
* sci-biology/mafft: drop x86-macosFabian Groffen2021-01-061-2/+2
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
* sci-biology/fasta: drop x86-macosFabian Groffen2021-01-061-2/+2
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
* */*: Update pypi (and github) remote-ids from HOMEPAGEMichał Górny2020-12-112-13/+17
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: reassing axs' packagesMichał Górny2020-12-091-4/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/embassy-emnu: Patch out -L/usr/lib for LLDDavid Seifert2020-11-021-22/+23
| | | | | | Closes: https://bugs.gentoo.org/731750 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/clustalw-mpi: Port to EAPI 7David Seifert2020-11-014-18/+32
| | | | | | | | | | * Rename USE flags to avoid underscore * Fix building against GCC 10 / -fno-common Closes: https://bugs.gentoo.org/695122 Closes: https://bugs.gentoo.org/706960 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/lagan: Port to EAPI 7David Seifert2020-11-0112-664/+550
| | | | | | | | | | | | | * Fix building against GCC 10 / -fno-common * Fix building against C99 / -O0 * Fix broken build system * Import patches from Debian Closes: https://bugs.gentoo.org/685736 Closes: https://bugs.gentoo.org/688700 Closes: https://bugs.gentoo.org/707404 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seaview: Remove old 4.5.4David Seifert2020-11-012-77/+0
| | | | | | Closes: https://bugs.gentoo.org/588506 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/seaview: Port to EAPI 7David Seifert2020-11-013-12/+203
| | | | | | | | | | * Fix building against GCC 10 / -fno-common * Fix building against Clang Closes: https://bugs.gentoo.org/707842 Closes: https://bugs.gentoo.org/741198 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/newick-utils: Port to EAPI 7David Seifert2020-11-015-24/+245
| | | | | | | | | | | | * Don't build static libraries by default * Fix GCC 10 / -fno-common * Disable automagic guile and lua Closes: https://bugs.gentoo.org/708534 Closes: https://bugs.gentoo.org/712312 Closes: https://bugs.gentoo.org/727986 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Patch out -L/usr/lib for LLDDavid Seifert2020-11-011-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731858 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Fix -fno-commonDavid Seifert2020-11-012-2/+632
| | | | | | Closes: https://bugs.gentoo.org/706414 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gmap: Remove old 2015.12.31.5David Seifert2020-11-012-21/+0
| | | | | | Closes: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gmap: Version bump to 2020.10.27David Seifert2020-11-013-0/+40
| | | | | | Bug: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/paml: Remove old 4.4c-r1David Seifert2020-11-012-48/+0
| | | | | | Closes: https://bugs.gentoo.org/706708 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/paml: Version bump to 4.9jDavid Seifert2020-11-014-0/+100
| | | | | | Bug: https://bugs.gentoo.org/706708 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/dialign-tx: Fix -fno-commonDavid Seifert2020-11-013-6/+49
| | | | | | | Closes: https://bugs.gentoo.org/707008 Closes: https://bugs.gentoo.org/727966 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/profphd: Port to EAPI 7David Seifert2020-10-272-17/+24
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/profphd: Remove old 1.0.39David Seifert2020-10-272-38/+0
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/muscle: Port to EAPI 7David Seifert2020-10-272-12/+9
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/unafold: Port to EAPI 7David Seifert2020-10-272-8/+22
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/phylip: Remove oldDavid Seifert2020-10-274-162/+0
| | | | | | | Closes: https://bugs.gentoo.org/707150 Closes: https://bugs.gentoo.org/727982 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>