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freebsd-ports/biology
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Yuri Victorovich 4d0e67e147 biology/taxonkit: update 0.15.0 → 0.15.1 
Reported by:	portscout
2023-12-19 23:02:18 -08:00
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abyss
*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2
2023-12-10 11:23:11 +01:00
ad2vcf
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artemis
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atac-seq
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augustus
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avida
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babel
biology/babel: Update WWW
2023-10-30 23:37:03 +01:00
bamtools
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bamutil
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barrnap
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bbmap
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bcf-score
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bcftools
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bedtools
biology/bedtools: Update to 2.31.1
2023-11-08 10:42:09 -06:00
bfc
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bifrost
biology/bifrost: Update to 1.3.1
2023-11-21 06:58:39 -06:00
bio-mocha
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bioawk
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biococoa
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biolibc
biology/biolibc: Update to 0.2.6
2023-10-28 06:21:35 -05:00
biolibc-tools
biology/biolibc-tools: Update to 0.1.4.13
2023-10-29 17:41:02 -05:00
bioparser
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biosig
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
biosoup
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biostar-tools
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bolt-lmm
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2023-12-12 20:03:50 +01:00
bowtie
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
bowtie2
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btllib
biology/btllib: update 1.6.2 → 1.7.0
2023-12-12 21:22:27 -08:00
bwa
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canu
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cd-hit
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cdbfasta
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checkm
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chip-seq
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clustal-omega
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clustalw
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cufflinks
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cytoscape
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ddocent
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diamond
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dsr-pdb
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edlib
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emboss
biology/emboss: fix build on powerpc*
2023-12-03 12:13:43 +01:00
erminej
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exonerate
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fasda
biology/fasda: Update to 0.1.5
2023-10-28 06:32:20 -05:00
fasta
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fasta3
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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
biology/fastq-trim: Update to 0.1.3
2023-10-28 06:34:21 -05:00
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
biology/gatk: update 4.4.0.0 → 4.5.0.0
2023-12-18 01:14:18 -08:00
gcta
biology/gcta: chase the upgrade of OpenBLAS
2023-12-12 20:03:50 +01:00
gemma
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2023-12-12 20:03:50 +01:00
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
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hisat2
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hmmer
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htslib
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hyphy
biology/hyphy: Update to 2.5.57
2023-11-14 20:09:46 -04:00
igv
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infernal
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iolib
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-01 23:11:47 +01:00
iqtree
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jalview
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jellyfish
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kallisto
biology/kallisto: Update to 0.50.1,1
2023-11-04 08:15:25 -05:00
kmcp
all: Bump PORTREVISION after lang/go* update
2023-12-07 02:22:10 +00:00
lamarc
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libbigwig
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libcombine
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libgff
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libgtextutils
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libneurosim
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libnuml
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libsbml
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libsedml
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linux-foldingathome
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locarna
biology/locarna: Fix build on 14.x and main
2023-12-13 23:11:55 -08:00
mafft
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mapm3
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mashmap
biology/mashmap: update 3.1.1 → 3.1.2
2023-12-06 00:34:56 -08:00
megahit
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metaeuk
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migrate
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minimap2
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mmseqs2
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molden
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mothur
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mrbayes
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mummer
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
muscle
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ncbi-blast+
devel/grpc: Update to 1.60.0
2023-12-15 01:03:10 +08:00
ncbi-cxx-toolkit
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ncbi-entrez-direct
all: Bump PORTREVISION after lang/go* update
2023-12-07 02:22:10 +00:00
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-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
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p5-TrimGalore
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paml
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pbbam
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pbseqan
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peak-classifier
biology/peak-classifier: Update to 0.1.4.13
2023-10-28 06:38:43 -05:00
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
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2023-12-12 20:03:50 +01:00
pooler
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primer3
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prodigal
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prodigy-lig
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protomol
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-01 23:11:47 +01:00
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-biosig
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
py-bx-python
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py-crossmap
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py-cutadapt
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py-deeptools
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py-deeptoolsintervals
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py-dna-features-viewer
biology/py-dna-features-viewer: Update to 3.1.3
2023-11-04 17:11:34 -05:00
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-htseq
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py-libnuml
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py-libsedml
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py-loompy
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py-macs2
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py-mrcfile
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py-multiqc
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py-ont-fast5-api
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py-orange3-bioinformatics
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py-orange3-single-cell
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py-pandas-charm
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py-py2bit
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py-pybigwig
biology/py-pybigwig: Update to 0.3.22
2023-12-16 07:59:37 -06:00
py-pyfaidx
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py-pyrodigal
biology/py-pyrodigal: update 3.1.1 → 3.2.1
2023-12-19 23:02:18 -08:00
py-pysam
biology/py-pysam: relax python version requirement
2023-12-03 14:51:05 +03:00
py-PySCeS
biology/py-PySCeS: Fix build by adding USES=localbase:ldflags
2023-12-14 00:43:06 -08:00
py-python-libsbml
biology/py-python-libsbml: relax python version requirement
2023-12-03 15:02:23 +03:00
py-pywgsim
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py-resdk
biology/py-resdk: relax chardet limitation
2023-12-08 21:55:13 +01:00
py-scikit-bio
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py-valerius
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py-xenaPython
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pyfasta
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python-nexus
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R-cran-Biobase
biology/R-cran-Biobase: New port
2023-12-15 13:55:44 +01:00
R-cran-BiocGenerics
biology/R-cran-BiocGenerics: New port
2023-12-15 13:55:44 +01:00
R-cran-BiocManager
biology/R-cran-BiocManager: New port
2023-12-15 13:55:43 +01:00
rainbow
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rampler
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readseq
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recombine
biology/recombine: Mark DEPRECATED
2023-12-17 14:11:36 +01:00
rna-seq
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ruby-bio
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rubygem-bio
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rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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salmon
devel/onetbb: Update to 2021.11.0
2023-11-28 12:35:02 +01:00
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
biology/seqio: Mark DEPRECATED
2023-12-17 14:11:36 +01:00
seqkit
all: Bump PORTREVISION after lang/go* update
2023-12-07 02:22:10 +00:00
seqtk
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seqwish
biology/seqwish: Add comment
2023-11-05 15:07:52 -08:00
sigviewer
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sim4
biology/sim4: fix EXPIRATION_DATE
2023-12-18 09:29:31 +01:00
slclust
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smithwaterman
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snpeff
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
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
biology/taxonkit: update 0.15.0 → 0.15.1
2023-12-19 23:02:18 -08:00
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
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unikmer
all: Bump PORTREVISION after lang/go* update
2023-12-07 02:22:10 +00:00
vcf2hap
biology/vcf2hap: Update to 0.1.6.7
2023-10-28 06:44:44 -05:00
vcf-split
biology/vcf-split: Update to 0.1.5.10
2023-10-28 06:41:39 -05:00
vcflib
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vcftools
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velvet
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viennarna
biology/viennarna: update 2.6.3 → 2.6.4
2023-11-03 15:02:11 -07:00
vsearch
biology/vsearch: Update to 2.26.1
2023-11-26 06:32:55 -06:00
vt
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wfa2-lib
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wise
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Makefile
biology/R-cran-Biobase: New port
2023-12-15 13:55:44 +01:00