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Jason W. Bacon 4fd08b5074 biology/mmseqs2: Update to 16.747.c6 
Numerous fixes and improvements since v13
Changes: https://github.com/soedinglab/MMseqs2/releases

PR:             283251
Reported by:    alster@vinterdalen.se
 		2025-01-15 09:06:03 -06:00
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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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abyss Mk/bsd.commands.mk: Use absolute path to define GMAKE 2024-12-29 12:34:56 +01:00
ad2vcf
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andi
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artemis Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
atac-seq all: remove support for expired FreeBSD 13.3 2025-01-01 17:09:59 +01:00
augustus */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
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 biology/bbmap: Update to 39.14 2025-01-13 15:50:59 -06:00
bcf-score */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
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 */*: bump PORTREVISION after the upgrade to Suitesparse 2025-01-11 11:02:35 +01:00
biosoup
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biostar-tools
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bolt-lmm
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bowtie
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bowtie2
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btllib
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bwa biology/bwa: small improvements 2025-01-06 17:29:54 +01:00
canu Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
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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coverm biology/coverm: fix build with char being unsigned 2024-12-31 14:59:43 +01:00
cufflinks
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cytoscape Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
ddocent Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
diamond
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dsr-pdb
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edlib
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emboss
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erminej Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
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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fastani
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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 Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
fasttree
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fastx-toolkit
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fermi-lite
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figtree Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
flash
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fluctuate
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freebayes
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garlic
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gatk Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
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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gkl Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
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
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igv Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
infernal
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iolib
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iqtree
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jalview Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
jellyfish
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kallisto
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kmcp
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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
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mafft
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mapm3
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mashmap
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mca-calling
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megahit
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metaeuk
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migrate
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minimap2
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mmseqs2 biology/mmseqs2: Update to 16.747.c6 2025-01-15 09:06:03 -06:00
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+ biology/ncbi-blast+: Update to 2.16.0 2025-01-14 11:43:59 -06:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: update 28.0.11 → 28.0.12 2025-01-07 01:29:09 -08:00
ncbi-entrez-direct
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ncbi-toolkit
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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-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-Das
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p5-Bio-Das-Lite
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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-TrimGalore
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p5-transdecoder
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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
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picard-tools Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
plink
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pooler
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preseq
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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-Genesis-PyAPI
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py-PySCeS
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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
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py-bx-python
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py-crossmap
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py-cutadapt biology/py-cutadapt: Update to 5.0 2025-01-10 16:35:23 +01:00
py-deeptools
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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-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-macs3
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py-mrcfile
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py-multiqc
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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
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py-pysam
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py-python-libsbml
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py-pywgsim
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py-resdk
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py-scikit-bio biology/py-scikit-bio: update 0.6.2 → 0.6.3 2025-01-13 19:26:05 -08:00
py-valerius
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py-xenaPython
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pyfasta
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python-nexus
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rainbow
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rampler
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readseq Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +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
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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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seqan-apps
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seqan1
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seqan3
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seqkit
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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 Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
spoa
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sra-tools Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
stacks
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star
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stringtie
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subread
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tRNAscan-SE
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tabixpp
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taxonkit
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treekin
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treepuzzle
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trimadap
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trimmomatic Mk/**java.mk: Convert bsd.java.mk to USES 2024-12-31 09:57:55 +01:00
ucsc-userapps
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ugene
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unikmer biology/unikmer: Update WWW 2025-01-05 20:01:04 -08:00
vcf-split
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vcf2hap
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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 2.29.2 2024-12-29 14:59:05 -06:00
vt
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wfa2-lib
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wise
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Makefile biology/ncbi-vdb: Remove expired port 2025-01-01 11:59:57 +01:00