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* sci-biology/tree-puzzle: drop unused toolchain-funcsSam James2022-04-261-2/+0
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/GBrowse: treecleanJakov Smolić2022-04-174-155/+0
| | | | | | | | Closes: https://bugs.gentoo.org/828702 Closes: https://bugs.gentoo.org/690042 Closes: https://bugs.gentoo.org/513594 Closes: https://bugs.gentoo.org/402849 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/plink: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/mrbayes: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/mosaik: [QA] fix tc-get* quotingSam James2022-03-201-3/+3
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/glimmer: [QA] fix tc-get* quotingSam James2022-03-201-4/+4
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/fasta: [QA] fix tc-get* quotingSam James2022-03-201-3/+3
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/blat: [QA] fix tc-get* quotingSam James2022-03-201-3/+3
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/fasta: fix broken README symlinkDavid Seifert2022-03-191-1/+1
| | | | | Closes: https://bugs.gentoo.org/835634 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/fasta: drop 36.3.5eDavid Seifert2022-03-193-154/+0
| | | | | | Closes: https://bugs.gentoo.org/648618 Closes: https://bugs.gentoo.org/828700 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/fasta: add 36.3.8hDavid Seifert2022-03-193-0/+145
| | | | | | Bug: https://bugs.gentoo.org/648618 Bug: https://bugs.gentoo.org/828700 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bioperl-run: update EAPI 5 -> 8David Seifert2022-03-192-41/+33
| | | | | Closes: https://bugs.gentoo.org/835362 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bioperl-network: update EAPI 5 -> 8David Seifert2022-03-192-31/+26
| | | | | | Closes: https://bugs.gentoo.org/298326 Bug: https://bugs.gentoo.org/835362 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bioperl: update EAPI 5 -> 8David Seifert2022-03-191-16/+13
| | | | | Bug: https://bugs.gentoo.org/835362 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: drop 2.29.2David Seifert2022-03-193-64/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.15David Seifert2022-03-192-0/+45
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.15David Seifert2022-03-192-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/foldingathome: add version 7.6.21Andrew Ammerlaan2022-03-012-0/+139
| | | | | | Closes: https://bugs.gentoo.org/757840 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/seqan: add version 3.1.0Andrew Ammerlaan2022-02-242-0/+32
| | | | | | Closes: https://bugs.gentoo.org/774702 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/STAR: unbundle htslib properlyDavid Seifert2022-02-192-0/+203
| | | | | Closes: https://bugs.gentoo.org/833770 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vcftools: add version 0.1.16Andrew Ammerlaan2022-02-192-0/+38
| | | | | | Closes: https://bugs.gentoo.org/833503 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/STAR: add version 2.7.10aAndrew Ammerlaan2022-02-192-0/+42
| | | | | | | | | Closes: https://bugs.gentoo.org/696714 Bug: https://bugs.gentoo.org/741152 Bug: https://bugs.gentoo.org/736056 Bug: https://bugs.gentoo.org/716300 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/embassy-vienna: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-topo: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-structure: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-signature: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-mse: update EAPI 7 -> 8David Seifert2022-02-142-10/+13
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-iprscan: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-hmmer: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-esim4: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-emnu: update EAPI 7 -> 8David Seifert2022-02-142-8/+11
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domsearch: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domalign: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-domainatrix: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-clustalomega: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-cbstools: update EAPI 7 -> 8David Seifert2022-02-142-7/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/emboss: update EAPI 7 -> 8David Seifert2022-02-142-9/+12
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/repeatmasker: treecleanJakov Smolić2022-02-103-67/+0
| | | | | Closes: https://bugs.gentoo.org/828701 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/repeatmasker-libraries: treecleanJakov Smolić2022-02-103-38/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/rmblast: treecleanJakov Smolić2022-02-103-57/+0
| | | | | | | | | | | | Closes: https://bugs.gentoo.org/515962 Closes: https://bugs.gentoo.org/579248 Closes: https://bugs.gentoo.org/664518 Closes: https://bugs.gentoo.org/711246 Closes: https://bugs.gentoo.org/716172 Closes: https://bugs.gentoo.org/457972 Closes: https://bugs.gentoo.org/724466 Closes: https://bugs.gentoo.org/828706 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/tree-puzzle: fix build system and MPIDavid Seifert2022-01-292-12/+375
| | | | | | | Closes: https://bugs.gentoo.org/690900 Closes: https://bugs.gentoo.org/810502 Closes: https://bugs.gentoo.org/814185 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: add forgotten runtime dependencyAndrew Ammerlaan2022-01-281-0/+1
| | | | | | Closes: https://bugs.gentoo.org/832186 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/augustus: add version 3.4.0Andrew Ammerlaan2022-01-272-0/+48
| | | | | | Closes: https://bugs.gentoo.org/515996 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/mrbayes: add version 3.2.7Andrew Ammerlaan2022-01-273-9/+56
| | | | | | Closes: https://bugs.gentoo.org/521510 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/gibbs: treecleanJakov Smolić2022-01-164-72/+0
| | | | | Bug: https://bugs.gentoo.org/829216 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/abyss: drop version 2.0.3Andrew Ammerlaan2022-01-133-76/+0
| | | | | | | Closes: https://bugs.gentoo.org/741154 Closes: https://bugs.gentoo.org/715718 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/abyss: add version 2.3.4Andrew Ammerlaan2022-01-132-0/+58
| | | | | | Closes: https://bugs.gentoo.org/646478 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/picard: treecleanJakov Smolić2022-01-084-212/+0
| | | | | | | Closes: https://bugs.gentoo.org/776298 Closes: https://bugs.gentoo.org/580176 Closes: https://bugs.gentoo.org/572142 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/biopython: drop 1.77David Seifert2021-12-302-62/+0
| | | | | | Closes: https://bugs.gentoo.org/757867 Closes: https://bugs.gentoo.org/780345 Signed-off-by: David Seifert <soap@gentoo.org>