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* biology/linux-foldingathome: Point MASTER_SITES to the new locationMateusz Piotrowski2024-08-121-1/+1
| | | | (cherry picked from commit be31db3b28cdf1175b5be76fd94a796830c01ef7)
* biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processorsJason W. Bacon2024-07-251-0/+3
| | | | | | Upstream supports specific architectures, mainly 64-bit and ARM Neon (cherry picked from commit f84c63104e8cde852cffab5b4702d8e5fb70a2c2)
* biology/gcta: Unbreak fetchJason W. Bacon2024-07-081-3/+3
| | | | | | Fix mysterious distinfo corruption (cherry picked from commit 84a6e7ec36ea62363eaf642fe9192c6dece13792)
* all: Bump after lang/go121 updateAshish SHUKLA2024-07-035-5/+5
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* biology/iqtree: Update to 2.3.5Joseph Mingrone2024-07-012-9/+8
| | | | | Release Notes: https://github.com/iqtree/iqtree2/releases/tag/v2.3.5 Sponsored by: The FreeBSD Foundation
* all: drop support for FreeBSD 13.2 which reached EOL todayRene Ladan2024-07-011-6/+0
| | | | | | | Thanks again to jbeich for noticing various things I overlooked. Reviewed by: acm, ashish, eduardo, ehaupt, eugen, jbeich, martymac, mat, nobukata, sunpoet, tagattie, yuri, arrowd, kde Differential Revision: https://reviews.freebsd.org/D45141
* */*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDSJason E. Hale2024-06-292-2/+4
| | | | | | | | Fix build when setuptools is removed from RUN_DEPENDS in Mk/Uses/python.mk. PR: 270510 Approved by: portmgr (blanket)
* */*: bump PORTREVISION after the upgrade to OpenBLASThierry Thomas2024-06-214-4/+4
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* biology/hyphy: Update to 2.5.62Joseph Mingrone2024-06-212-4/+4
| | | | | Commit log: https://github.com/veg/hyphy/compare/2.5.61...2.5.62 Sponsored by: The FreeBSD Foundation
* biology/py-cutadapt: update to 4.9Philippe Audeoud2024-06-202-4/+4
| | | | changelog: https://cutadapt.readthedocs.io/en/stable/changes.html#v4-9-2024-06-19
* biology/py-scikit-bio: update 0.6.0 → 0.6.1Yuri Victorovich2024-06-193-14/+4
| | | | Reported by: portscout
* biology/libsbml: Fix build with libxml2 2.12.0+Daniel Engberg2024-06-182-1/+6
| | | | | PR: 279752 Obtained from: https://github.com/sbmlteam/libsbml/commit/a3e217851f18d3c5e8e2b0082fb98176738491e8
* biology/py-gffutils: update 0.11.1 → 0.13Yuri Victorovich2024-06-172-5/+11
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* biology/phyml: fix build on non-amd64Piotr Kubaj2024-06-161-1/+1
| | | | cc: error: unsupported option '-msse3' for target 'powerpc64-unknown-freebsd14.1'
* all: Bump after lang/go121 updateAshish SHUKLA2024-06-155-3/+5
| | | | MFH: 2024Q2
* biology/unikmer: update 0.19.1 → 0.20.0Älven2024-06-113-17/+14
| | | | PR: 279674
* biology/py-pywgsim: fix buildRuslan Makhmatkhanov2024-06-071-1/+1
| | | | | | cython dependency not available at post-patch stage. Use post-configure instead Approved by: portmgr (blanket approval)
* biology/ncbi-cxx-toolkit: update 28.0.4 → 28.0.5Yuri Victorovich2024-06-062-4/+4
| | | | Reported by: portscout
* biology/py-pywgsim: unbreak with python3.11Ruslan Makhmatkhanov2024-06-041-7/+4
| | | | | | | make it recreate the source with newer cython PR: 275494 Approved by: portmgr (blanket approval)
* biology/py-pywgsim: unbreak bulk -aAntoine Brodin2024-06-031-2/+8
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* biology/py-pywgsim: Limit to python 3.10Jason W. Bacon2024-06-031-1/+2
| | | | | | | Nontrivial changes needed for python 3.11 Abandoned upstream Reported by: pkg-fallout
* biology/biostar-tools: Update to 1.11Jason W. Bacon2024-06-032-4/+2
| | | | | | Drop abandonware py-pywgsim dep Reported by: pkg-fallout
* biology/metaeuk: update 6 → 7Yuri Victorovich2024-06-012-15/+12
| | | | Reported by: portscout
* biology/gcta: Unbreak build on 14.x aarch64Jason W. Bacon2024-05-284-3/+33
| | | | | | Missing #include <cstdint> in a few files Reported by: pkg-fallout
* biology/stacks: Unbreak build on aarch64Jason W. Bacon2024-05-281-0/+11
| | | | | | ARM clang is intolerant of implicit demotions in initializers Reported by: pkg-fallout
* biology/minimap2: Unbreak build on aarch64Jason W. Bacon2024-05-281-0/+3
| | | | | | Remove unsupports -msse flags Reported by: pkg-fallout
* biology/py-cutadapt: update to 4.8Philippe Audeoud2024-05-282-5/+5
| | | | While here, take maintainership
* biology/py-PySCeS: update 1.1.1 → 1.2.1Yuri Victorovich2024-05-263-16/+28
| | | | Reported by: portscout
* biology/py-pyrodigal: update 3.4.0 → 3.4.1Älven2024-05-263-18/+18
| | | | PR: 279310
* biology/cytoscape: Broken on i386Yuri Victorovich2024-05-261-0/+1
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* biology/unikmer: Add PORTSCOUT lineYuri Victorovich2024-05-251-0/+2
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* biology/bowtie2: Update to 2.5.4Jason W. Bacon2024-05-242-4/+4
| | | | | | | A few bug fixes and minor enhancements Changes: https://github.com/BenLangmead/bowtie2/releases Reported by: portscout
* biology/vcflib: add upstream reference for zig >= 0.11Jan Beich2024-05-201-0/+1
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* biology/py-pyrodigal: update 3.3.0 → 3.4.0Yuri Victorovich2024-05-202-4/+4
| | | | Reported by: portscout
* biology/ad2vcf: Update to 0.1.6.19Jason W. Bacon2024-05-192-5/+5
| | | | | Use xt_fopen() to support all common compression tools A few other minor improvements
* biology/biolibc: Update to 0.2.6.4Jason W. Bacon2024-05-192-5/+5
| | | | bl_sam_copy(): Make sure all fields are properly initialized
* biology/seqwish: update 0.7.9 → 0.7.10Yuri Victorovich2024-05-182-4/+4
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* biology/seqkit: update 2.8.1 → 2.8.2Yuri Victorovich2024-05-182-9/+8
| | | | Reported by: portscout
* biology/iqtree: Update to 2.3.4Joseph Mingrone2024-05-163-16/+5
| | | | | Release notes: https://github.com/iqtree/iqtree2/releases/tag/v.2.3.4 Sponsored by: The FreeBSD Foundation
* biology/hyphy: Update to 2.5.61Joseph Mingrone2024-05-162-4/+4
| | | | | | Release notes: https://github.com/veg/hyphy/releases/tag/2.5.61 Commit log: https://github.com/veg/hyphy/compare/2.5.56...2.5.61 Sponsored by: The FreeBSD Foundation
* biology/mothur: update 1.48.0 → 1.48.1Yuri Victorovich2024-05-162-4/+4
| | | | Reported by: portscout
* all: Bump after lang/go121 updateAshish SHUKLA2024-05-135-5/+5
| | | | MFH: 2024Q2
* biology/R-cran-BiocManager: Update version 1.30.22=>1.30.23Muhammad Moinur Rahman2024-05-112-4/+4
| | | | Changelog: https://github.com/Bioconductor/BiocManager/releases/tag/v1.30.23
* biology/ncbi-cxx-toolkit: update 28.0.3 → 28.0.4Yuri Victorovich2024-05-072-5/+4
| | | | Reported by: portscout
* biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dirJason W. Bacon2024-05-051-1/+2
| | | | | | | Reduces I/O during builds PR: 278751 Reported by: diizzy
* biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dirJason W. Bacon2024-05-051-3/+3
| | | | | | | Reduces I/O during builds PR: 278739 Reported by: diizzy
* biology/pbseqan: Remove expired portRene Ladan2024-05-055-700/+0
| | | | 2024-05-05 biology/pbseqan: Upstream merged into SeqAn project: Use biology/seqan
* biology/vsearch: Update to 2.28.1Jason W. Bacon2024-05-012-4/+4
| | | | | | | A few bug fixes and enhancements Changes: https://github.com/torognes/vsearch/releases Reported by: portscout
* */*: chase SuiteSparse’s upgradeThierry Thomas2024-04-292-1/+2
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* biology/ngs-sdk: Attempt to fix build on i386Yuri Victorovich2024-04-281-3/+23
| | | | Reported by: fallout
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