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freebsd-ports/biology
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Jason W. Bacon 001947d3e5 biology/vsearch: Update to 2.22.1 
Add the derep_smallmem command for dereplication with less memory usage
Changes:    https://github.com/torognes/vsearch/releases

Reported by:    portscout
2022-09-21 11:24:14 -05:00
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abyss
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ad2vcf
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artemis
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avida
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babel
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bamtools
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bamutil
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bbmap
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bcftools
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bedtools
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bfc
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bio-mocha
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bioawk
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biococoa
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biolibc
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biolibc-tools
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bioparser
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biosig
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bowtie
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bwa
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canu
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checkm
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ddocent
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diamond
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edlib
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emboss
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exonerate
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fastahack
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fastdnaml
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fastool
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fastp
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fastq-trim
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fastqc
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fasttree
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fastx-toolkit
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figtree
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flash
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fluctuate
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freebayes
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garlic
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gatk
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gcta
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gemma
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generand
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gff2ps
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gffread
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gmap
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gperiodic
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graphlan
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groopm
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haplohseq
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hhsuite
biology/hhsuite: Broken on armv7
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hisat2
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hmmer
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htslib
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hyphy
biology/hyphy: Update to 2.5.42
2022-09-19 18:10:39 -03:00
igv
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infernal
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iolib
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kallisto
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kmcp
all: Bump PORTREVISION after lang/go{118,119} update
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lamarc
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libbigwig
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libgff
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libgtextutils
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libneurosim
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libnuml
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linux-foldingathome
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minimap2
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molden
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mothur
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mrbayes
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mummer
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muscle
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ncbi-blast+
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ncbi-cxx-toolkit
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ncbi-entrez-direct
all: Bump PORTREVISION after lang/go{118,119} update
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ncbi-toolkit
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ncbi-vdb
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ngs-sdk
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-transdecoder
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p5-TrimGalore
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paml
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pbseqan
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peak-classifier
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pear-merger
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phrap
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phred
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phyml
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picard-tools
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plink
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pooler
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primer3
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prodigal
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protomol
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psi88
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py-bcbio-gff
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py-biom-format
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py-biopython
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py-deeptoolsintervals
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py-dna-features-viewer
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py-dnaio
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py-ete3
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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py-gtfparse
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py-hits
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py-libnuml
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py-loompy
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py-macs2
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py-PySCeS
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py-python-libsbml
*/*: Update path set in BUILD_DEPENDS for CMake
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py-pywgsim
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py-resdk
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rainbow
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rampler
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readseq
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recombine
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ruby-bio
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rubygem-bio
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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sam2pairwise
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samtools
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scrm
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seaview
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seqan
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seqan1
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seqan3
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seqan-apps
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seqio
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seqkit
all: Bump PORTREVISION after lang/go{118,119} update
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seqtk
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sigviewer
Mk/Uses: always use colon for build/run suffix
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sim4
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slclust
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smithwaterman
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snpeff
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spoa
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sra-tools
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stacks
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star
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stringtie
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subread
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tabixpp
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taxonkit
all: Bump PORTREVISION after lang/go{118,119} update
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treekin
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treepuzzle
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trimadap
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trimmomatic
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tRNAscan-SE
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ucsc-userapps
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ugene
Mk/Uses: always use colon for build/run suffix
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unikmer
all: Bump PORTREVISION after lang/go{118,119} update
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vcf2hap
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vcf-split
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vcflib
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vcftools
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velvet
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viennarna
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vsearch
biology/vsearch: Update to 2.22.1
2022-09-21 11:24:14 -05:00
vt
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wise
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Makefile
biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching
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