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* sci-biology/bioperl-db: adjust mysql_install_db locationThomas Deutschmann2021-03-201-14/+29
| | | | | | | Since commit 755be857e3051, mysql_install_db location has changed. Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org>
* */*: Add proxied="yes" for non-@gentoo.org peopleMichał Górny2021-03-161-1/+1
| | | | | | | | | | | | Done via: find -name metadata.xml -exec xml ed -P -L \ -a '/pkgmetadata/maintainer[substring(email, string-length(email) - string-length("@gentoo.org") + 1) != "@gentoo.org"]' \ -t attr -n proxied -v yes {} + Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Normalize metadata.xml filesMichał Górny2021-03-167-7/+6
| | | | | | | | | | | Normalize quoting, replace '>' with entities, replace unnecessary entities, remove trailing empty lines. Done via: find -name metadata.xml -exec xml ed -P -L -d //none {} + Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bfast: Port to EAPI 7David Seifert2021-03-134-26/+207
| | | | | | Closes: https://bugs.gentoo.org/625490 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Remove accidentally committed fileDavid Seifert2021-03-131-188/+0
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Port to EAPI 7David Seifert2021-03-132-2/+190
| | | | | Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-emnu: depend on ncurses unconditionallyDavid Seifert2021-03-131-3/+5
| | | | | | Closes: https://bugs.gentoo.org/752216 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-emnu: 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-hmmer: 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-hmmer: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/741182 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-topo: 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-topo: Fix building against clang/LLDDavid Seifert2021-03-131-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731926 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-iprscan: 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-iprscan: Fix building against clang/LLDDavid Seifert2021-03-131-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731908 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-signature: 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-signature: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731894 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-structure: 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-structure: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731866 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-vienna: 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-vienna: Fix building against clang/LLDDavid Seifert2021-03-131-15/+27
| | | | | | Closes: https://bugs.gentoo.org/731852 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-mse: Fix building against clang/LLDDavid Seifert2021-03-131-21/+18
| | | | | | Closes: https://bugs.gentoo.org/731850 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domainatrix: 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-domainatrix: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731760 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-cbstools: 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-cbstools: Fix building against clang/LLDDavid Seifert2021-03-131-17/+17
| | | | | | Closes: https://bugs.gentoo.org/731758 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domalign: 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-domalign: Fix building against clang/LLDDavid Seifert2021-03-131-14/+17
| | | | | | Closes: https://bugs.gentoo.org/731756 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
* 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>