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freebsd-ports/biology
History
Po-Chuan Hsieh b90b53dcb2
biology/libsbml: Update to 5.20.4 
Changes:	https://github.com/sbmlteam/libsbml/releases
2024-09-09 02:36:57 +08:00
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abyss
biology/abyss: update 2.3.7 → 2.3.8
2024-07-22 17:34:22 -07:00
ad2vcf
biology/ad2vcf: Update to 0.1.6.19
2024-05-19 08:41:41 -05:00
andi
biology/andi: New ports: Efficient estimation of evolutionary distances
2024-09-07 14:31:10 -07:00
artemis
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atac-seq
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augustus
*/*: chase SuiteSparse’s upgrade
2024-04-29 22:08:56 +02:00
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
biology/biolibc: Update to 0.2.6.4
2024-05-19 08:40:24 -05:00
biolibc-tools
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bioparser
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biosig
biology/{.py-}biosig: update 2.6.0 → 2.6.1
2024-08-05 07:37:01 -07:00
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 PORTVERSION of math/nlopt consumers
2024-08-25 15:33:16 +02:00
bowtie
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bowtie2
biology/bowtie2: Update to 2.5.4
2024-05-24 06:33:53 -05:00
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
biology/checkm: update 1.2.0 → 1.2.2
2024-04-23 01:40:35 -07:00
chip-seq
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clustal-omega
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clustalw
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cufflinks
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cytoscape
biology/cytoscape: Broken on i386
2024-05-25 18:45:24 -07:00
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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fermi-lite
biology/fermi-lite: fix build on powerpc64le
2024-08-13 11:40:45 +02:00
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 COMMENT
2024-08-04 13:13:15 -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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gkl
biology/gkl: New port: Accelerated kernel library for genomics
2024-08-04 13:09:41 -07:00
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 2.3.6
2024-09-07 22:53:14 -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
2024-08-09 06:24:08 +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: Update to 5.20.4
2024-09-09 02:36:57 +08:00
libsedml
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linux-foldingathome
biology/linux-foldingathome: Point MASTER_SITES to the new location
2024-08-12 14:58:05 +02:00
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
biology/mothur: update 1.48.0 → 1.48.1
2024-05-16 01:56:44 -07:00
mrbayes
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mummer
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muscle
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ncbi-blast+
devel/grpc: Update to 1.65.4
2024-08-15 18:55:25 +08:00
ncbi-cxx-toolkit
biology/ncbi-cxx-toolkit: update 28.0.7 → 28.0.8
2024-09-07 21:10:05 -07:00
ncbi-entrez-direct
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
ncbi-toolkit
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ncbi-vdb
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ngs-sdk
biology/ngs-sdk: Attempt to fix build on i386
2024-04-28 00:10:02 -07:00
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
biology/peak-classifier: Clean up USES=python
2024-04-05 08:43:40 +08:00
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
biology/prodigy-lig: update 1.1.0 → 1.1.1
2024-04-26 22:55:21 -07:00
protomol
graphics/tiff: Update to 4.6.0
2024-04-27 14:44:59 +02:00
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
biology/py-biopython: Update to 1.83
2024-04-08 02:29:37 +00:00
py-biosig
biology/{.py-}biosig: update 2.6.0 → 2.6.1
2024-08-05 07:37:01 -07:00
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 3.5.1 → 3.5.2
2024-09-05 01:48:51 -07:00
py-pysam
biology/py-pysam: update 0.22.0 → 0.22.1
2024-04-25 07:52:08 -07:00
py-PySCeS
biology/py-PySCeS: update 1.2.1 → 1.2.2
2024-08-03 01:27:31 -07:00
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
biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25
2024-09-08 19:28:55 +02:00
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
2024-08-09 06:24:08 +00:00
seqtk
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seqwish
biology/seqwish: update 0.7.9 → 0.7.10
2024-05-18 10:29:58 -07:00
sigviewer
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slclust
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smithwaterman
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snpeff
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spoa
biology/spoa: Broken on i386
2024-04-11 21:05:12 -07:00
sra-tools
cleanup: remove occurrences of WITH_DEBUG
2024-04-12 08:04:05 +02:00
stacks
biology/stacks: Unbreak build on aarch64
2024-05-28 16:17:25 -05:00
star
biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
2024-05-05 09:58:47 -05:00
stringtie
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subread
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tabixpp
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taxonkit
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
treekin
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treepuzzle
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trimadap
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trimmomatic
biology/trimmomatic: Release to ports@
2024-04-05 19:12:17 -05:00
tRNAscan-SE
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ucsc-userapps
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ugene
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unikmer
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
vcf2hap
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vcf-split
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vcflib
biology/vcflib: add upstream reference for zig >= 0.11
2024-05-20 16:42:43 +02:00
vcftools
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velvet
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viennarna
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vsearch
biology/vsearch: Update to 2.28.1
2024-05-01 08:41:05 -05:00
vt
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wfa2-lib
biology/wfa2-lib: fix build without libomp
2024-08-04 14:00:47 +02:00
wise
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Makefile
biology/andi: New ports: Efficient estimation of evolutionary distances
2024-09-07 14:31:10 -07:00