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* biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8Po-Chuan Hsieh2023-12-252-5/+5
| | | | | | - Update LICENSE_FILE Changes: https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
* biology/hyphy: Update to 2.5.58Joseph Mingrone2023-12-233-4/+6
| | | | | Changes: https://github.com/veg/hyphy/releases/tag/2.5.58 Sponsored by: The FreeBSD Foundation
* biology/taxonkit: update 0.15.0 → 0.15.1Yuri Victorovich2023-12-202-7/+6
| | | | Reported by: portscout
* biology/py-pyrodigal: update 3.1.1 → 3.2.1Yuri Victorovich2023-12-202-4/+4
| | | | Reported by: portscout
* biology/gatk: update 4.4.0.0 → 4.5.0.0Yuri Victorovich2023-12-182-8/+8
| | | | ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0
* biology/sim4: fix EXPIRATION_DATERene Ladan2023-12-181-1/+1
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* biology/recombine: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-4/+8
| | | | | | | - Upstream last release was in 2002 - Upstream advises to use bioloby/lamarc - Set EXPIRATION_DATE 2024-01-17 - Pet portclippy
* biology/seqio: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-7/+11
| | | | | | - Upstream last release was in 2000 - Set EXPIRATION_DATE 2024-01-17 - Pet portclippy
* biology/sim4: Mark DEPRECATEDMuhammad Moinur Rahman2023-12-171-0/+3
| | | | | - Upstream last update was in 2005 - Set EXPIRATION_DATE 2024-01-17
* biology/py-pybigwig: Update to 0.3.22Jason W. Bacon2023-12-163-4/+33
| | | | | | | No real changes from 0.3.21 Add patch to resolve conflict with roundup() macro in sys/param.h Reported by: pkg-fallout
* biology/R-cran-Biobase: New portMuhammad Moinur Rahman2023-12-154-0/+24
| | | | | | | Functions that are needed by many other packages or which replace R functions. WWW: https://bioconductor.org/packages/Biobase
* biology/R-cran-BiocGenerics: New portMuhammad Moinur Rahman2023-12-154-0/+21
| | | | | | The package defines many S4 generic functions used in Bioconductor. WWW: https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html
* biology/R-cran-BiocManager: New portMuhammad Moinur Rahman2023-12-154-0/+22
| | | | | | | | | The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data. WWW: https://bioconductor.github.io/BiocManager/
* devel/grpc: Update to 1.60.0Po-Chuan Hsieh2023-12-141-0/+1
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
* biology/py-PySCeS: Fix build by adding USES=localbase:ldflagsYuri Victorovich2023-12-141-1/+1
| | | | Reported by: fallout
* biology/locarna: Fix build on 14.x and mainYuri Victorovich2023-12-141-0/+1
| | | | | | The code uses the STL method that was remved in C++17. Reported by: fallout
* biology/btllib: update 1.6.2 → 1.7.0Yuri Victorovich2023-12-133-7/+7
| | | | Reported by: portscout
* */*: bump PORTREVISION after the upgrade of OpenBLASThierry Thomas2023-12-123-3/+3
| | | | PR: 273219
* biology/gcta: chase the upgrade of OpenBLASEijiro Shibusawa2023-12-125-3/+72
| | | | | | | | | GCTA should modify the LAPACK functios calls, this is a temporary fix. See <https://github.com/jianyangqt/gcta/issues/59>. PR: 273219 Approved by: jwb@
* */*: bump PORTREVISION after the upgrade of MPICH to 4.1.2Thierry Thomas2023-12-101-0/+1
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* biology/py-resdk: relax chardet limitationThierry Thomas2023-12-081-1/+1
| | | | | | | It accepts chardet-5.2.0. PR: 275630 Approved by: yuri@ (maintainer)
* all: Bump PORTREVISION after lang/go* updateAshish SHUKLA2023-12-075-3/+5
| | | | PR: 274405
* biology/mashmap: update 3.1.1 → 3.1.2Yuri Victorovich2023-12-062-4/+4
| | | | Reported by: portscout
* biology/py-python-libsbml: relax python version requirementRuslan Makhmatkhanov2023-12-031-1/+1
| | | | | | | | | According to [1] python-libsbml supports Python 3.11 since version 5.19.2 [1] https://github.com/sbmlteam/python-libsbml/releases/tag/v5.19.2 PR: 275494 Approved by: portmgr (blanket)
* biology/py-pysam: relax python version requirementRuslan Makhmatkhanov2023-12-031-1/+1
| | | | | | | | | According to [1] pysam support Python 3.11 since version 0.21.0 [1] https://github.com/pysam-developers/pysam/releases/tag/v0.21.0 PR: 275494 Approved by: portmgr (blanket)
* biology/emboss: fix build on powerpc*Piotr Kubaj2023-12-031-0/+10
| | | | | | | | | | ajfileio.c:271:7: warning: call to undeclared function 'ajSysFuncFgets'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] cp = ajSysFuncFgets(&buff[ipos], isize, file->fp); ^ ajfileio.c:271:5: error: incompatible integer to pointer conversion assigning to 'const char *' from 'int' [-Wint-conversion] cp = ajSysFuncFgets(&buff[ipos], isize, file->fp); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated.
* devel/onetbb: Update to 2021.11.0Ganael LAPLANCHE2023-11-281-1/+1
| | | | | | and bump dependent ports' revisions. Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.11.0
* biology/vsearch: Update to 2.26.1Jason W. Bacon2023-11-262-4/+4
| | | | | | | A few minor enhancements Changes: https://github.com/torognes/vsearch/releases Reported by: portscout
* biology/bifrost: Update to 1.3.1Jason W. Bacon2023-11-213-15/+4
| | | | | | | Minor bugfix release Changes: https://github.com/pmelsted/bifrost/releases Reported by: portscout
* biology/seqkit: update 2.6.0 → 2.6.1Yuri Victorovich2023-11-192-8/+8
| | | | Reported by: portscout
* biology/hyphy: Update to 2.5.57Joseph Mingrone2023-11-152-4/+4
| | | | | Changes: https://github.com/veg/hyphy/releases/tag/2.5.57 Sponsored by: The FreeBSD Foundation
* biology/seqkit: update 2.5.1 → 2.6.0Yuri Victorovich2023-11-132-9/+8
| | | | Reported by: portscout
* biology/vsearch: Update to 2.25.0Jason W. Bacon2023-11-122-5/+4
| | | | | | chimeras_denovo: Allow user to specify mismatch tolerance Changes: https://github.com/torognes/vsearch/releases
* biology/bedtools: Update to 2.31.1Jason W. Bacon2023-11-082-4/+4
| | | | | | Code updates for modern compilers Changes: https://github.com/arq5x/bedtools2/releases
* biology/py-pyrodigal: update 3.1.0 → 3.1.1Yuri Victorovich2023-11-072-4/+4
| | | | Reported by: portscout
* biology/hyphy: Update to 2.5.56Joseph Mingrone2023-11-072-4/+4
| | | | | | Changes: https://github.com/veg/hyphy/releases/tag/2.5.56 https://github.com/veg/hyphy/releases/tag/2.5.55 Sponsored by: The FreeBSD Foundation
* */*: Update WWW to use HTTPS for sourceforge.net projectsRodrigo Osorio2023-11-065-5/+5
| | | | | | | | Homepage link is permanent redirected to its HTTPS counterpart Issue reported by repology : https://repology.org/repository/freebsd/problems Approved by: portmgr (blanket) PR: 274888
* biology/py-pyrodigal: update 2.2.0 → 3.1.0Yuri Victorovich2023-11-052-6/+7
| | | | Reported by: portscout
* biology/seqwish: Add commentYuri Victorovich2023-11-051-1/+1
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* biology/py-dna-features-viewer: Update to 3.1.3Jason W. Bacon2023-11-042-5/+4
| | | | | | | | Latest biopython and matplotlib compatibility Changes: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/releases Reported by: portscout
* biology/kallisto: Update to 0.50.1,1Jason W. Bacon2023-11-043-5/+14
| | | | | | | | Update kallisto index version to 13 A few other new features Changes: https://github.com/pachterlab/kallisto/releases Reported by: portscout
* biology/viennarna: update 2.6.3 → 2.6.4Yuri Victorovich2023-11-032-9/+14
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* */*: Bump PORTREVISION for Ghostscript 10 changeMichael Osipov2023-11-031-0/+1
| | | | | | Reported by: sunpoet Approved by: jrm (mentor), sunpoet Differential Revision: https://reviews.freebsd.org/D42412
* */*: Update WWW to use HTTPS for sourceforge.net projectsRodrigo Osorio2023-11-012-2/+2
| | | | Homepage link is permanent redirected to its HTTPS counterpart
* */*: bump portrevision to chase CHOLMOD’s upgradeThierry Thomas2023-10-311-1/+1
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* biology/babel: Update WWWRodrigo Osorio2023-10-301-3/+2
| | | | Homepage link is dead,use last webarchive instead.
* biology/py-resdk: update 19.0.1 → 20.0.0Yuri Victorovich2023-10-302-4/+4
| | | | Reported by: portscout
* biology/emboss: Optionize mysql supportMuhammad Moinur Rahman2023-10-291-5/+6
| | | | | | | | The port builds fine without mysql and as MySQL57 is reaching end of life so optionize MYSQL so that other flavors can be used and still there is an available pkg for this port. Approved by: portmgr (blanket)
* biology/biolibc-tools: Update to 0.1.4.13Jason W. Bacon2023-10-292-5/+5
| | | | Updates for new libxtend API
* biology/vcf2hap: Update to 0.1.6.7Jason W. Bacon2023-10-283-5/+5
| | | | Updates for new libxtend API
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