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* 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>
* sci-biology/wise: eutils->epatchSam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/velvet: eutils--Sam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.18-prefix, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/rmblast: eutils->epatchSam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/psipred: eutils->epatchSam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/plink: eutils--Sam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.18-prefix, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/ncbi-tools: eutils->epatchSam James2021-04-181-1/+1
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/mrbayes: eutils->epatchSam James2021-04-181-2/+2
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/fasta: eutils->epatchSam James2021-04-181-1/+1
| | | | | Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/mira: eutils--Sam James2021-04-161-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* 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>