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* sci-biology/ncbi-tools: add missing pkgconfig (B)DEPENDSam James2021-04-121-2/+5
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/probcons: Port to EAPI 7David Seifert2021-04-051-13/+9
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mothur: Port to EAPI 7David Seifert2021-04-051-18/+17
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/raxml: Port to EAPI 7David Seifert2021-04-052-17/+12
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/sibsim4: Port to EAPI 7David Seifert2021-04-052-14/+31
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/repeatmasker-libraries: Port to EAPI 7David Seifert2021-04-051-12/+7
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/update-blastdb: Port to EAPI 7David Seifert2021-04-051-10/+5
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/cutg: Port to EAPI 7David Seifert2021-04-051-20/+13
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/glimmer: Port to EAPI 7David Seifert2021-04-052-22/+24
| | | | | | Closes: https://bugs.gentoo.org/731892 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/glimmer: Remove old 3.02David Seifert2021-04-055-195/+0
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gatk: Port to EAPI 7David Seifert2021-04-051-11/+5
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/treeviewx: Port to EAPI 7David Seifert2021-04-044-42/+31
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopython: Use optfeature_header() instead of custom elogAndreas Sturmlechner2021-04-041-6/+5
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/bioperl: fix variable referencesSam James2021-04-031-3/+3
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* 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>