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Code Issues Releases Activity
freebsd-ports/biology
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Yuri Victorovich c1ef3af576 biology/btllib: update 1.7.2 → 1.7.3 
Reported by:	portscout
2024-07-27 13:19:18 -07:00
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abyss
biology/abyss: update 2.3.7 → 2.3.8
2024-07-22 17:34:22 -07:00
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
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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
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bfc
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bifrost
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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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biosoup
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biostar-tools
biology/biostar-tools: Update to 1.11
2024-06-03 06:38:30 -05:00
bolt-lmm
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
bowtie
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bowtie2
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btllib
biology/btllib: update 1.7.2 → 1.7.3
2024-07-27 13:19:18 -07:00
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
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erminej
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exonerate
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fasda
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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
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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
biology/gatk: Fix fetch
2024-07-20 01:36:53 -07:00
gcta
biology/gcta: Unbreak fetch
2024-07-08 17:04:44 -05:00
gemma
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
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 2.5.62
2024-06-21 13:58:09 -03:00
igv
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infernal
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iolib
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iqtree
biology/iqtree: Update to 2.3.5
2024-07-01 18:28:31 -03:00
jalview
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jellyfish
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kallisto
biology/kallisto: Update to 0.51.0,1
2024-07-27 07:02:57 -05:00
kmcp
all: Bump after lang/go121 update
2024-07-03 08:29:54 +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
devel/automake: Update to 1.17
2024-07-20 13:27:02 +02:00
libnuml
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libsbml
biology/libsbml: Fix build with libxml2 2.12.0+
2024-06-18 12:05:09 +08:00
libsedml
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linux-foldingathome
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locarna
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mafft
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mapm3
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mashmap
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megahit
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metaeuk
biology/metaeuk: update 6 → 7
2024-06-01 01:10:52 -07:00
migrate
biology/migrate: fix build on !x86
2024-07-09 12:04:31 +02:00
minimap2
biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
2024-07-20 14:55:08 -05:00
mmseqs2
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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
biology/ncbi-cxx-toolkit: update 28.0.5 → 28.0.6
2024-07-06 18:27:07 -07:00
ncbi-entrez-direct
all: Bump after lang/go121 update
2024-07-03 08:29:54 +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
biology/p5-TrimGalore: Update to 0.6.10
2024-07-23 11:01:28 -04:00
paml
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pbbam
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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
biology/phyml: fix build on non-amd64
2024-06-16 17:25:18 +02:00
picard-tools
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plink
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
pooler
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primer3
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prodigal
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prodigy-lig
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protomol
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psi88
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py-bcbio-gff
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py-biom-format
biology/py-biom-format: update 2.1.10 → 2.1.16
2024-07-13 11:06:57 -07:00
py-biopython
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py-biosig
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py-bx-python
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py-crossmap
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py-cutadapt
biology/py-cutadapt: update to 4.9
2024-06-20 10:38:00 +02:00
py-deeptools
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py-deeptoolsintervals
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py-dna-features-viewer
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py-dnaio
biology/py-dnaio: Update to 1.2.1
2024-07-04 09:15:39 +00:00
py-ete3
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py-Genesis-PyAPI
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py-gffutils
biology/py-gffutils: update 0.11.1 → 0.13
2024-06-16 18:20:35 -07:00
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-macs3
all: drop support for FreeBSD 13.2 which reached EOL today
2024-07-01 22:27:23 +02:00
py-mrcfile
biology/py-mrcfile: update 1.5.2 → 1.5.3
2024-07-26 01:57:55 -07:00
py-multiqc
devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml
2024-07-07 16:05:33 +08:00
py-newick
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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
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py-pyfaidx
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py-pyrodigal
biology/py-pyrodigal: update 3.5.0 → 3.5.1
2024-07-22 17:34:23 -07:00
py-pysam
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py-PySCeS
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py-python-libsbml
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py-pywgsim
biology/py-pywgsim: fix build
2024-06-07 11:11:35 +03:00
py-resdk
biology/py-resdk: update 21.1.0 → 21.2.0
2024-07-12 01:58:00 -07:00
py-scikit-bio
biology/py-scikit-bio: update 0.6.1 → 0.6.2
2024-07-12 22:17:53 -07:00
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
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R-cran-BiocGenerics
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R-cran-BiocManager
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rainbow
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rampler
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readseq
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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 2021.13.0
2024-07-04 13:39:44 +02:00
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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seqkit
all: Bump after lang/go121 update
2024-07-03 08:29:54 +00:00
seqtk
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seqwish
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sigviewer
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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
biology/stacks: Unbreak build on aarch64
2024-05-28 16:17:25 -05:00
star
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stringtie
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subread
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tabixpp
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taxonkit
biology/taxonkit: update 0.16.0 → 0.17.0
2024-07-04 09:32:16 -07:00
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 after lang/go121 update
2024-07-03 08:29:54 +00:00
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
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vt
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wfa2-lib
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wise
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Makefile
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