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2023-03-09all: Bump PORTREVISION after lang/go119 updateDmitri Goutnik5-5/+5
Direct commit to quarterly to bump Go ports revisions after 61a665d2d8d2 Approved by: ports-secteam (blanket)
2023-02-17all: Bump PORTREVISION after lang/go119 updateDmitri Goutnik5-3/+5
Direct commit to quarterly to bump Go ports revisions after f30271912e48 Approved by: riggs (ports-secteam)
2022-12-31biology/lamarc: Refactor after wxgtk28 removalMuhammad Moinur Rahman1-7/+7
- Pet portclippy
2022-12-30biology/py-biosig: New port: Library for reading and writing different ↵Yuri Victorovich4-0/+36
biosignal data format
2022-12-30biology/biosig: Update 2.4.3 -> 2.5.0Yuri Victorovich3-5/+53
Reported by: portscout
2022-12-26biology/taxonkit: Update 0.14.0 -> 0.14.1Yuri Victorovich2-7/+6
Reported by: portscout
2022-12-26biology/unikmer: Update 0.19.0 -> 0.19.1Yuri Victorovich2-7/+6
Reported by: portscout
2022-12-25biology/hyphy: Update to 2.5.43Joseph Mingrone2-4/+4
Sponsored by: The FreeBSD Foundation
2022-12-22biology/py-pyrodigal: Update 2.0.2 -> 2.0.3Yuri Victorovich2-5/+5
Reported by: portscout
2022-12-19biology/snpeff: Update to 5.1Jason W. Bacon2-4/+4
Unbreak fetch, which depends on an unversioned distfile Requested version tags upstream and looking at other build options
2022-12-19biology/pooler: update to 1.86Silas S. Brown2-4/+5
ChangeLog: https://github.com/ssb22/PrimerPooler/commit/0d2b55459d0689ad505a34fe54d2d7214890b13d * fix spurious memory error on M1 Mac PR: 268445 Reported by: silas-freebsd@flatline.org.uk (maintainer)
2022-12-13biology/biolibc-tools: Update to 0.1.4.1Jason W. Bacon2-4/+5
deromanize: Check for NULL field to prevent crash in some situations Take optional input file as second argument
2022-12-12biology/biolibc-tools: Update to 0.1.4Jason W. Bacon3-5/+6
Add deromanize subcommand to convert Roman numeral chromosome IDs fastx-stats: Report standard deviation for read length Changes: https://github.com/auerlab/biolibc-tools/releases
2022-12-12biology/rna-seq: Metaport for RNA-Seq analysisJason W. Bacon4-0/+30
Metaport to install tools for typical RNA-Seq analysis, including QC, adapter trimming, alignment, and differential analysis.
2022-12-12biology/fasda: Fast and simple differential analysisJason W. Bacon5-0/+44
FASDA aims to provide a fast and simple differential analysis tool that just works and does not require any knowledge beyond basic Unix command-line skills. The code is written entirely in C to maximize efficiency and portability, and to provide a simple command-line user interface.
2022-12-11biology/fastq-trim: Update to 0.1.2Jason W. Bacon3-7/+10
Minor enhancements, fixes for SunOS Changes: https://github.com/auerlab/fastq-trim/releases
2022-12-11biology/vcf-split: Update to 0.1.5-4Jason W. Bacon2-4/+5
Update for biolibc API changes
2022-12-11biology/peak-classifier: Update to 0.1.4-5Jason W. Bacon3-5/+5
Update for biolibc API changes
2022-12-11biology/biolibc: Update to 0.2.4Jason W. Bacon2-4/+4
Minor enhancements Changes: https://github.com/auerlab/biolibc/releases
2022-12-11all: Bump PORTREVISION after lang/go{118,119} updateDmitri Goutnik5-4/+5
2022-12-10biology/cytoscape: Broken on armv6, armv7Yuri Victorovich1-0/+3
Reported by: fallout
2022-12-10biology/metaeuk: Fix build on systems withour OpenMP enabledYuri Victorovich1-4/+4
Reported by: fallout
2022-12-08biology/libcombine: Update 0.2.19 -> 0.2.20Yuri Victorovich3-10/+10
Reported by: portscout
2022-12-06biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder ↵Yuri Victorovich4-0/+50
for genomes and metagenomes
2022-12-06Revert: "all: deprecate ports depending on expired security/py-keyrings.alt"Rene Ladan2-6/+0
This reverts commit f9f811816c9a50a19570ef4ee66dc6e3f43baec5. security/py-keyrings.alt was updated to use supported dependencies in commit a16d8f14ce3bbcae7b17b690069593b5b0c7fb9e
2022-12-05biology/py-biopython: Update to 1.80Wen Heping2-5/+5
PR: 268106 Reported by: wen@ Approved by: maintainer
2022-12-02biology/metaeuk: Broken on systems where OpenMP isn't enabledYuri Victorovich1-0/+4
Reported by: fallout
2022-12-01biology/metaeuk: append missing bracketPiotr Kubaj1-1/+1
2022-12-01biology/metaeuk: fix build without libomp and disable -m{arch,cpu}=nativePiotr Kubaj1-0/+7
2022-11-29biology/taxonkit: Update 0.13.0 -> 0.14.0Yuri Victorovich2-7/+6
Reported by: portscout
2022-11-27*/*: bump PORTREVISION after the upgrade of math/suitesparse*Thierry Thomas1-1/+1
PR: 267742
2022-11-26biology/gatk: Update 4.2.6.1 -> 4.3.0.0Yuri Victorovich2-8/+6
2022-11-26biology/cytoscape: Fix buildYuri Victorovich1-1/+1
maven-3.6.3 should be used.
2022-11-26biology/metaeuk: New port: Gene discovery and annotation for large-scale ↵Yuri Victorovich4-0/+47
eukaryotic metagenomics
2022-11-25biology/augustus: New port: Genome annotation toolYuri Victorovich7-0/+1619
2022-11-24biology/barrnap: Update descrYuri Victorovich1-6/+8
2022-11-24biology/barrnap: New port: BAsic Rapid Ribosomal RNA PredictorYuri Victorovich5-0/+47
2022-11-24biology/cytoscape: Unbreak by re-adding and using maven-3.6.3Yuri Victorovich1-2/+0
Cytoscape was broken by the maven update.
2022-11-24biology/megahit: Add cmake patch to respect ports build flagsJason W. Bacon2-0/+18
Removes agressive optimizations hard-coded upstream
2022-11-22biology/megahit: Ultra-fast single-node metagenomics assemblyJason W. Bacon5-0/+45
MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction.
2022-11-17graphics/proj: Update to 9.1.0Loïc Bartoletti1-0/+1
Release notes: https://proj.org/news.html#id37 Also remove proj-data dependency. You can use proj to retrieve data or install graphics/proj-data manually.
2022-11-12biology/paml: Update to 4.10.6Joseph Mingrone3-15/+6
https://github.com/abacus-gene/paml/releases/tag/v4.10.6 Sponsored by: The FreeBSD Foundation
2022-11-10biology/py-pysam: Update 0.19.1 -> 0.20.0Yuri Victorovich2-11/+12
Reported by: portscout
2022-11-09biology/bowtie2: fix build on powerpc64*Piotr Kubaj1-2/+2
2022-11-04biology/bowtie2: Update to 2.5.0Jason W. Bacon3-8/+12
Performance improvements and minor improvements Changes: https://github.com/BenLangmead/bowtie2/tags Reported by: portscout
2022-10-26biology/biosig: Make sure __LITTLE_ENDIAN is defined in include files.Stephen Montgomery-Smith2-4/+8
Bump port revision. PR: 267372 Approved by: yuri@freebsd.org
2022-10-22*/*: Bump PORTREVISION for consumers of libunistringDaniel Engberg1-1/+1
Reported by: jbeich
2022-10-21biology/libcombine: New port: C++ library for working with the COMBINE ↵Yuri Victorovich7-0/+119
archive format
2022-10-12biology/tRNAscan-SE: Update to 2.0.11Motomichi Matsuzaki4-10/+14
ChangeLog: http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt PR: 266966
2022-10-12biology/infernal: Update to 1.1.4Motomichi Matsuzaki4-41/+11
ChangeLog: http://eddylab.org/infernal/RELEASE-1.1.4.md PR: 266967
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