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* sci-biology/vcftools: drop 0.1.14Sam James2022-07-023-90/+0
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/bioperl-db: update EAPI 6 -> 8David Seifert2022-07-021-13/+17
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: drop 0.12.4David Seifert2022-07-022-34/+0
| | | | | | Closes: https://bugs.gentoo.org/809662 Closes: https://bugs.gentoo.org/846221 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: sync live ebuildDavid Seifert2022-07-021-7/+42
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/HTSeq: add 2.0.2David Seifert2022-07-022-0/+69
| | | | | | Bug: https://bugs.gentoo.org/809662 Bug: https://bugs.gentoo.org/846221 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mafft: drop 7.305David Seifert2022-06-253-78/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/aaindex: update EAPI 6 -> 8David Seifert2022-06-191-5/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prints: update EAPI 6 -> 8David Seifert2022-06-191-4/+4
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/rebase: update EAPI 6 -> 8David Seifert2022-06-191-11/+11
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/primer3: update EAPI 6 -> 8David Seifert2022-06-192-30/+54
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prosite: update EAPI 6 -> 8David Seifert2022-06-191-6/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mafft: add 7.490David Seifert2022-06-192-0/+63
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/fastx_toolkit: update EAPI 6 -> 8David Seifert2022-06-191-7/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/libgtextutils: update EAPI 6 -> 8David Seifert2022-06-191-9/+3
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: drop 1.13, 1.15David Seifert2022-06-193-96/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: drop 1.13, 1.15David Seifert2022-06-193-90/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: enable py3.11David Seifert2022-06-191-1/+1
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/pysam: drop 0.17.0David Seifert2022-06-192-67/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mosaik: fix build with GCC 12Sam James2022-06-132-0/+12
| | | | | Closes: https://bugs.gentoo.org/851669 Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/pysam: add 0.19.1David Seifert2022-06-102-0/+67
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bcftools: add 1.15.1David Seifert2022-06-102-0/+43
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/samtools: add 1.15.1David Seifert2022-06-102-0/+48
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/biopython: Use slot for dev-python/psycopgMichał Górny2022-06-041-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/seqan: Keyword 3.1.0 x86, #834863Jakov Smolić2022-06-011-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-biology/seqan: [QA] use tc-check-openmp correctlyDavid Seifert2022-05-161-1/+5
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/cutg: [QA] eend without argumentThomas Bracht Laumann Jespersen2022-05-131-3/+3
| | | | | Signed-off-by: Thomas Bracht Laumann Jespersen <t@laumann.xyz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/STAR: fix GCC 12 buildDavid Seifert2022-05-072-1/+26
| | | | | Closes: https://bugs.gentoo.org/840586 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/STAR: drop 2.5.3aDavid Seifert2022-05-073-166/+0
| | | | | | | Closes: https://bugs.gentoo.org/716300 Closes: https://bugs.gentoo.org/736056 Closes: https://bugs.gentoo.org/741152 Signed-off-by: David Seifert <soap@gentoo.org>
* 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>