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* biology/migrate: Fix extractNuno Teixeira2024-03-271-1/+1
| | | | | | | | | | Extract fails on aarch64 with error: (sample) "dynsections.js: Cannot restore extended attributes: com.apple.quarantine com.apple.quarantine: No such file or directory" tar: Error exit delayed from previous errors.- Fix extract with: --no-same-owner --no-same-permissions
* biology/migrate: Update to 5.0.5Nuno Teixeira2024-03-273-31/+27
| | | | | | | | | - Switch to DISTVERSION - Add license - Pet portlint, portclippy and portfmt - Take maintainership ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY
* lang/go: Change DEFAULT to 1.21Muhammad Moinur Rahman2024-03-245-3/+5
| | | | | PR: 277776 Approved by: portmgr (exp-run)
* biology/minimap2: Move man page to share/manYasuhiro Kimura2024-03-223-4/+5
| | | | Approved by: portmgr (blanket)
* biology/prodigy-lig: update 1.0.1 → 1.1.0Yuri Victorovich2024-03-212-5/+4
| | | | Reported by: portscout
* biology/bifrost: Update to 1.3.5Jason W. Bacon2024-03-182-4/+4
| | | | | | | | A few new features and bug fixes Some important changes in CLI behavior Changes: https://github.com/pmelsted/bifrost/releases Reported by: portscout
* py-cutadapt: Update to 4.7Jason W. Bacon2024-03-162-5/+5
| | | | | | | | | | Send error message to stderr Add support for single-ended uBAM Drop Python 3.7 Changes: https://cutadapt.readthedocs.io/en/stable/changes.html Reported by: portscout
* biology/minimap2: Update to 2.27Jason W. Bacon2024-03-134-9/+8
| | | | | | | Several new features and a few bug fixes Changes: https://github.com/lh3/minimap2/releases Reported by: portscout
* biology/seqkit: update 2.7.0 → 2.8.0Yuri Victorovich2024-03-122-8/+8
| | | | Reported by: portscout
* devel/grpc: Update to 1.62.0Po-Chuan Hsieh2024-03-091-1/+1
| | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Broken ports are skipped: - science/py-tensorflow - sysutils/apache-mesos Changes: https://github.com/grpc/grpc/releases
* biology/taxonkit: update 0.15.1 → 0.16.0Yuri Victorovich2024-03-082-7/+6
| | | | Reported by: portscout
* biology/seqkit: update 2.6.1 → 2.7.0Yuri Victorovich2024-03-082-9/+8
| | | | Reported by: portscout
* biology/py-pyrodigal: update 3.2.2 → 3.3.0Yuri Victorovich2024-03-082-4/+4
| | | | Reported by: portscout
* biology/ncbi-cxx-toolkit: update 28.0.0 → 28.0.2Yuri Victorovich2024-03-082-4/+4
| | | | Reported by: portscout
* biology/locarna: Move man pages to share/manNuno Teixeira2024-03-032-28/+30
| | | | Approved by: portmgr (blanket)
* biology/abyss: Move man pages to share/manNuno Teixeira2024-03-032-2/+3
| | | | Approved by: portmgr (blanket)
* biology/vsearch: Move man pages to share/manNuno Teixeira2024-03-021-1/+3
| | | | Approved by: portmgr (blanket)
* biology/viennarna: Move man pages to share/manNuno Teixeira2024-03-022-34/+35
| | | | Approved by: portmgr (blanket)
* biology/vcftools: Move man pages to share/manNuno Teixeira2024-03-022-2/+3
| | | | Approved by: portmgr (blanket)
* biology/vcflib: Move man pages to share/manNuno Teixeira2024-03-023-92/+99
| | | | Approved by: portmgr (blanket)
* biology/vcf2hap: Move man pages to share/manNuno Teixeira2024-03-021-2/+3
| | | | Approved by: portmgr (blanket)
* biology/vcf-split: Move man pages to share/manNuno Teixeira2024-03-021-2/+3
| | | | Approved by: portmgr (blanket)
* biology/treekin: Move man pages to share/manNuno Teixeira2024-03-021-2/+3
| | | | Approved by: portmgr (blanket)
* biology/scrm: Move man pages to share/manNuno Teixeira2024-03-021-1/+3
| | | | Approved by: portmgr (blanket)
* biology/samtools: Move man pages to share/manNuno Teixeira2024-03-022-42/+44
| | | | Approved by: portmgr (blanket)
* biology/peak-classifier: Move man pages to share/manNuno Teixeira2024-03-022-5/+8
| | | | Approved by: portmgr (blanket)
* biology/minimap2: Move man pages to share/manNuno Teixeira2024-03-023-4/+5
| | | | Approved by: portmgr (blanket)
* biology/jellyfish: Move man pages to share/manNuno Teixeira2024-03-022-2/+3
| | | | Approved by: portmgr (blanket)
* biology/generand: Move man pages to share/manNuno Teixeira2024-03-021-1/+4
| | | | Approved by: portmgr (blanket)
* biology/fastq-trim: Move man pages to share/manNuno Teixeira2024-03-022-69/+70
| | | | Approved by: portmgr (blanket)
* biology/fasda: Move man pages to share/manNuno Teixeira2024-03-022-5/+7
| | | | Approved by: portmgr (blanket)
* biology/biosig: Move man pages to share/manNuno Teixeira2024-03-022-12/+13
| | | | Approved by: portmgr (blanket)
* biology/biolibc-tools: Move man pages to share/manNuno Teixeira2024-03-022-14/+16
| | | | Approved by: portmgr (blanket)
* biology/bcftools: Move man pages to share/manNuno Teixeira2024-03-022-1/+3
| | | | Approved by: portmgr (blanket)
* biology/ad2vcf: Move man pages to share/manNuno Teixeira2024-03-021-1/+3
| | | | Approved by: portmgr (blanket)
* devel/py-setuptools-scm: update to 8.0.4Charlie Li2024-02-294-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | Directory and PORTNAME changed to match normalised name in release tarball; consumers updated to match. Although setuptools itself is specified as a run dependency in the Python package metadata, it is currently left out here to prevent environment pollution until at least PR 270510 is committed. Additionally, this version of setuptools-scm requires setuptools>=61, which means this version is only meant for USE_PYTHON=pep517 ports as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58 also after PR 270510. science/py-emmet-core is switched to devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8. devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to RUN_DEPENDS to compensate. Further details: https://wiki.freebsd.org/Python/setuptools Reported by: yuri Co-authored by: matthew Exp-run by: antoine (earlier iteration) Approved by: yuri (science/py-emmet-core, previous iteration) PR: 272134 Differential Revision: https://reviews.freebsd.org/D39288
* biology/py-macs3: Update to 3.0.1Jason W. Bacon2024-02-286-23/+18
| | | | | Minor bug fix release Changes: https://github.com/macs3-project/MACS/releases
* biology/pooler: Moved man to share/manMuhammad Moinur Rahman2024-02-221-1/+5
| | | | Approved by: portmgr (blanket)
* biology/mafft: Moved man to share/manMuhammad Moinur Rahman2024-02-223-3/+4
| | | | Approved by: portmgr (blanket)
* biology/iolib: Moved man to share/manMuhammad Moinur Rahman2024-02-222-24/+26
| | | | Approved by: portmgr (blanket)
* biology/infernal: Moved man to share/manMuhammad Moinur Rahman2024-02-222-11/+13
| | | | Approved by: portmgr (blanket)
* biology/hmmer: Moved man to share/manMuhammad Moinur Rahman2024-02-222-21/+23
| | | | Approved by: portmgr (blanket)
* biology/exonerate: Moved man to share/manMuhammad Moinur Rahman2024-02-222-4/+6
| | | | Approved by: portmgr (blanket)
* devel/grpc: Update to 1.61.1Po-Chuan Hsieh2024-02-211-1/+1
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
* */*: Replace format=bsdtar with format=ustar in tar archive operationsYuri Victorovich2024-02-191-1/+1
| | | | | | | | | | ... because the undocumented format bsdtar adds paxheaders on some systems, therefore breaking the fetch. The documentation for format=bsdtar should be added: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=277139 Approved by: portmgr (blanket unbreak)
* */*: bump PORTREVISION after OpenMPI upgradeThierry Thomas2024-02-181-1/+1
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* biology/biostar-tools: Update to 1.10.1_3Jason W. Bacon2024-02-163-15/+18
| | | | | Add sra-tools to metaport deps on aarch64 Clean up pkg-desc
* devel/boost: bump consumers after library updateDima Panov2024-02-134-4/+4
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* biology/py-bx-python: update 0.10.0 → 0.11.0Yuri Victorovich2024-02-122-4/+4
| | | | Reported by: portscout
* all: Bump PORTREVISION after lang/go* updateAshish SHUKLA2024-02-115-4/+5
| | | | PR: 276530
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