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* */*: 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
* biology/vcf-split: Update to 0.1.5.10Jason W. Bacon2023-10-282-5/+5
| | | | Updates for new libxtend API
* biology/peak-classifier: Update to 0.1.4.13Jason W. Bacon2023-10-282-6/+6
| | | | Updates for new libxtend API
* biology/fastq-trim: Update to 0.1.3Jason W. Bacon2023-10-282-4/+4
| | | | | | | | | | | fastq-scum: Add zstd and lz4 support Add low_qual_base_count update for paired end reads Clean up and expand final output format A few other minor improvements Updates for latest libxtend API Improvements to test script Changes: https://github.com/auerlab/fastq-trim/releases
* biology/fasda: Update to 0.1.5Jason W. Bacon2023-10-282-4/+4
| | | | | | | | | | | | | abundance: Update stringtie command to also produce gene-level abundances Output 0 for effective length for now to clearly indicate that it's invalid normalize: Add --debug option Updates for latest libxtend API Test -> Yeast-test Add Mouse-test suite with multiple mouse data options Streamline test scripts Changes: https://github.com/auerlab/fasda/releases
* biology/biolibc: Update to 0.2.6Jason W. Bacon2023-10-283-4/+7
| | | | | | | Updates for libxtend 0.2.0 API Add full list of functions to biolibc(3) man page Other documentation improvements Changes: https://github.com/auerlab/biolibc/releases
* biology/vsearch: Update to 2.24.0Jason W. Bacon2023-10-273-6/+14
| | | | | | | Upstream code cleanup Changes: https://github.com/torognes/vsearch/releases Reported by: portscout
* */*: chase the upgrade of CHOLMODThierry Thomas2023-10-201-1/+1
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* biology/bowtie2: Update to 2.5.2Jason W. Bacon2023-10-182-5/+6
| | | | | | | A few bug fixes Changes: https://github.com/BenLangmead/bowtie2/releases Reported by: portscout
* biology/gcta: Add temporary hack for building on aarch64Jason W. Bacon2023-10-151-1/+12
| | | | | | | | | | | | Add USE_GCC to work around this issue with clang: /usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/ \ plink2_base.h:1008:23: error: argument to '__builtin_neon_vshrq_n_v' \ must be a constant integer return R_CAST(VecW, _mm_srli_epi64(R_CAST(__m128i, vv), ct)); /usr/lib/clang/14.0.5/include/arm_neon.h:25260:24: note: expanded from \ macro 'vshrq_n_u64' __ret = (uint64x2_t) __builtin_neon_vshrq_n_v((int8x16_t)__s0, __p1, 51);
* */*: chase the upgrade of SuiteSparseThierry Thomas2023-10-152-2/+2
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* biology/gcta: Update to 1.94.1Jason W. Bacon2023-10-1414-200/+218
| | | | | | | Too many changes since v1.26 to list here Changes: https://yanglab.westlake.edu.cn/software/gcta/#Download Reported by: pkg-fallout
* biology/mashmap: disable on powerpcPiotr Kubaj2023-10-111-0/+1
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* biology/p5-BioPerl: Update to 1.007008Po-Chuan Hsieh2023-10-113-11/+8
| | | | | | | - Update WWW - Sort *_DEPENDS Changes: https://metacpan.org/dist/BioPerl/changes
* biology/bifrost: Update to 1.3.0Jason W. Bacon2023-10-113-6/+5
| | | | | | | | | | | Performance and memory efficiency improvements A few new features Note: New index format incompatible with previous versions Changes: https://github.com/pmelsted/bifrost/releases Reported by: portscout
* biology/py-pysam: update 0.21.0 → 0.22.0Yuri Victorovich2023-10-062-4/+4
| | | | Reported by: portscout
* biology/rubygem-bio: Update to 2.0.5Po-Chuan Hsieh2023-09-302-4/+4
| | | | Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
* biology/libsbml: Update to 5.20.2Po-Chuan Hsieh2023-09-302-4/+4
| | | | Changes: https://github.com/sbmlteam/libsbml/releases
* biology/wfa2-lib: Update to 2.3.4Jason W. Bacon2023-09-295-7/+24
| | | | | | | A few bug fixes Changes: https://github.com/smarco/WFA2-lib/releases Reported by: portscout
* biology/mothur: Remove CC/CPP/CXX exportsMuhammad Moinur Rahman2023-09-281-3/+0
| | | | | USES=llvm now by default exports CC/CPP/CXX so remove those Approved by: portmgr (blanket)
* devel/boost*: bump all consumers after 1.83.0Dima Panov2023-09-274-4/+4
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* /*: bump PORTREVISION after the upgrade of SuiteSparseThierry Thomas2023-09-202-1/+2
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* biology/kmcp: update 0.9.3 → 0.9.4Yuri Victorovich2023-09-182-7/+6
| | | | Reported by: portscout
* biology/seqan3: update 3.2.0 → 3.3.0Yuri Victorovich2023-09-103-23/+35
| | | | | PR: 273670 Reported by: Lorenzo Salvadore <salvadore@freebsd.org>
* biology/pooler: Update to 1.88Jason W. Bacon2023-09-102-4/+4
| | | | | | | | | Fix infinite loop Changes: https://ssb22.user.srcf.net/pooler/#changes PR: 273604 Reported by: silas-freebsd@flatline.org.uk
* all: Bump PORTREVISION after lang/go* updateDmitri Goutnik2023-09-085-3/+5
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* biology/peak-classifier: Clean up USES=pythonPo-Chuan Hsieh2023-09-061-1/+1
| | | | | Approved by: portmgr (blanket) With hat: python
* biology/hyphy: Update to 2.5.53Joseph Mingrone2023-09-052-4/+4
| | | | | Changes: https://github.com/veg/hyphy/releases/tag/2.5.53 Sponsored by: The FreeBSD Foundation
* biology/iqtree: Update to 2.2.2.7Joseph Mingrone2023-09-053-14/+16
| | | | | Changes: https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7 Sponsored by: The FreeBSD Foundation
* biology/spoa: update 4.0.7 → 4.1.0Yuri Victorovich2023-08-294-128/+21
| | | | Reported by: portscout
* biology/bioparser: update 3.0.15 → 3.1.0Yuri Victorovich2023-08-292-4/+6
| | | | Reported by: portscout
* biology/biosoup: Install cmake filesYuri Victorovich2023-08-292-6/+7
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* biology/py-resdk: update 19.0.0 → 19.0.1Yuri Victorovich2023-08-282-4/+4
| | | | Reported by: portscout
* biology/ncbi-blast+: Update to 2.14.1Jason W. Bacon2023-08-263-6/+19
| | | | | | | A few minor fixes and enhancements Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/ Reported by: portscout
* biology/seqwish: Add commentYuri Victorovich2023-08-251-0/+2
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* biology/py-resdk: update 18.0.0 → 19.0.0Yuri Victorovich2023-08-252-4/+4
| | | | Reported by: portscout
* biology/taxonkit: Update 0.14.2 → 0.15.0Yuri Victorovich2023-08-222-7/+6
| | | | Reported by: portscout
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