| .. |
|
abyss
|
all: drop support for expired FreeBSD 14.0
|
2024-10-01 20:56:20 +02:00 |
|
ad2vcf
|
|
|
|
andi
|
biology/andi: New ports: Efficient estimation of evolutionary distances
|
2024-09-07 14:31:10 -07:00 |
|
artemis
|
|
|
|
atac-seq
|
|
|
|
augustus
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
*/*: Bump dependencioes after devel/jsoncpp update
|
2024-09-12 09:20:06 -07:00 |
|
bamutil
|
|
|
|
barrnap
|
|
|
|
bbmap
|
|
|
|
bcf-score
|
|
|
|
bcftools
|
|
|
|
bedtools
|
|
|
|
bfc
|
|
|
|
bifrost
|
|
|
|
bio-mocha
|
|
|
|
bioawk
|
|
|
|
biococoa
|
|
|
|
biolibc
|
|
|
|
biolibc-tools
|
|
|
|
bioparser
|
|
|
|
biosig
|
all: drop support for expired FreeBSD 14.0
|
2024-10-01 20:56:20 +02:00 |
|
biosoup
|
|
|
|
biostar-tools
|
biology/biostar-tools: Update to 1.11
|
2024-06-03 06:38:30 -05:00 |
|
bolt-lmm
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
bowtie
|
|
|
|
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
|
|
|
|
canu
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
cd-hit
|
|
|
|
cdbfasta
|
|
|
|
checkm
|
|
|
|
chip-seq
|
|
|
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
coverm
|
biology/coverm: New port: Read coverage calculator for metagenomics
|
2024-10-04 20:09:27 -07:00 |
|
cufflinks
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
cytoscape
|
biology/cytoscape: Broken on i386
|
2024-05-25 18:45:24 -07:00 |
|
ddocent
|
|
|
|
diamond
|
|
|
|
dsr-pdb
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
edlib
|
|
|
|
emboss
|
|
|
|
erminej
|
|
|
|
exonerate
|
|
|
|
fasda
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
|
|
|
fastani
|
biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation
|
2024-09-20 20:03:29 -07:00 |
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
|
|
|
fastq-trim
|
|
|
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
fermi-lite
|
biology/fermi-lite: Add ONLY_FOR_ARCHS line
|
2024-09-19 14:05:26 -07:00 |
|
figtree
|
|
|
|
flash
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
|
|
|
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
|
|
|
|
gff2ps
|
|
|
|
gffread
|
|
|
|
gkl
|
biology/gkl: New port: Accelerated kernel library for genomics
|
2024-08-04 13:09:41 -07:00 |
|
gmap
|
|
|
|
gperiodic
|
|
|
|
graphlan
|
|
|
|
groopm
|
|
|
|
haplohseq
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
hhsuite
|
|
|
|
hisat2
|
|
|
|
hmmer
|
|
|
|
htslib
|
|
|
|
hyphy
|
biology/hyphy: Update to 2.5.62
|
2024-06-21 13:58:09 -03:00 |
|
igv
|
|
|
|
infernal
|
|
|
|
iolib
|
|
|
|
iqtree
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
jalview
|
|
|
|
jellyfish
|
|
|
|
kallisto
|
biology/kallisto: Update to 0.51.1,1
|
2024-09-19 17:46:47 -05:00 |
|
kmcp
|
all: Bump after lang/go121 update
|
2024-08-09 06:24:08 +00:00 |
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libcombine
|
|
|
|
libgff
|
|
|
|
libgtextutils
|
|
|
|
libneurosim
|
devel/automake: Update to 1.17
|
2024-07-20 13:27:02 +02:00 |
|
libnuml
|
|
|
|
libsbml
|
biology/libsbml: Update to 5.20.4
|
2024-09-09 02:36:57 +08:00 |
|
libsedml
|
|
|
|
linux-foldingathome
|
biology/linux-foldingathome: Point MASTER_SITES to the new location
|
2024-08-12 14:58:05 +02:00 |
|
locarna
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
mashmap
|
|
|
|
megahit
|
|
|
|
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
|
|
|
|
molden
|
|
|
|
mothur
|
all: drop support for expired FreeBSD 14.0
|
2024-10-01 20:56:20 +02:00 |
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
devel/grpc: Update to 1.66.1
|
2024-09-16 04:09:34 +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
|
all: drop support for expired FreeBSD 14.0
|
2024-10-01 20:56:20 +02:00 |
|
ncbi-vdb
|
|
|
|
ngs-sdk
|
|
|
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Cluster
|
|
|
|
p5-Bio-Coordinate
|
|
|
|
p5-Bio-Das
|
|
|
|
p5-Bio-Das-Lite
|
|
|
|
p5-Bio-DB-EMBL
|
|
|
|
p5-Bio-DB-NCBIHelper
|
|
|
|
p5-Bio-FeatureIO
|
|
|
|
p5-Bio-GFF3
|
|
|
|
p5-Bio-Glite
|
|
|
|
p5-Bio-Graphics
|
|
|
|
p5-Bio-MAGETAB
|
|
|
|
p5-Bio-NEXUS
|
|
|
|
p5-Bio-Phylo
|
|
|
|
p5-Bio-SCF
|
|
|
|
p5-Bio-Variation
|
|
|
|
p5-BioPerl
|
|
|
|
p5-BioPerl-Run
|
|
|
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
biology/p5-TrimGalore: Update to 0.6.10
|
2024-07-23 11:01:28 -04:00 |
|
paml
|
|
|
|
pbbam
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
peak-classifier
|
|
|
|
pear-merger
|
|
|
|
phrap
|
|
|
|
phred
|
|
|
|
phyml
|
biology/phyml: fix build on non-amd64
|
2024-06-16 17:25:18 +02:00 |
|
picard-tools
|
|
|
|
plink
|
*/*: bump PORTREVISION after the upgrade to OpenBLAS
|
2024-06-21 19:49:24 +02:00 |
|
pooler
|
|
|
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
biology/prodigy-lig: update 1.1.1 → 1.1.2
|
2024-10-04 02:15:23 -07:00 |
|
protomol
|
|
|
|
psi88
|
|
|
|
py-bcbio-gff
|
|
|
|
py-biom-format
|
biology/py-biom-format: update 2.1.10 → 2.1.16
|
2024-07-13 11:06:57 -07:00 |
|
py-biopython
|
|
|
|
py-biosig
|
biology/{.py-}biosig: update 2.6.0 → 2.6.1
|
2024-08-05 07:37:01 -07:00 |
|
py-bx-python
|
|
|
|
py-crossmap
|
|
|
|
py-cutadapt
|
biology/py-cutadapt: update to 4.9
|
2024-06-20 10:38:00 +02:00 |
|
py-deeptools
|
|
|
|
py-deeptoolsintervals
|
|
|
|
py-dna-features-viewer
|
|
|
|
py-dnaio
|
biology/py-dnaio: Update to 1.2.1
|
2024-07-04 09:15:39 +00:00 |
|
py-ete3
|
|
|
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
biology/py-gffutils: update 0.11.1 → 0.13
|
2024-06-16 18:20:35 -07:00 |
|
py-goatools
|
|
|
|
py-gtfparse
|
|
|
|
py-hits
|
|
|
|
py-htseq
|
|
|
|
py-libnuml
|
|
|
|
py-libsedml
|
|
|
|
py-loompy
|
|
|
|
py-macs2
|
|
|
|
py-macs3
|
biology/py-macs3: Update to 3.0.2
|
2024-09-14 08:23:32 -05:00 |
|
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
|
|
|
|
py-ont-fast5-api
|
|
|
|
py-orange3-bioinformatics
|
|
|
|
py-orange3-single-cell
|
|
|
|
py-pandas-charm
|
|
|
|
py-py2bit
|
|
|
|
py-pybigwig
|
|
|
|
py-pyfaidx
|
|
|
|
py-pyrodigal
|
biology/py-pyrodigal: update 3.5.1 → 3.5.2
|
2024-09-05 01:48:51 -07:00 |
|
py-pysam
|
|
|
|
py-PySCeS
|
biology/py-PySCeS: update 1.2.1 → 1.2.2
|
2024-08-03 01:27:31 -07:00 |
|
py-python-libsbml
|
|
|
|
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
|
|
|
|
py-xenaPython
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
R-cran-Biobase
|
|
|
|
R-cran-BiocGenerics
|
|
|
|
R-cran-BiocManager
|
biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25
|
2024-09-08 19:28:55 +02:00 |
|
rainbow
|
|
|
|
rampler
|
|
|
|
readseq
|
|
|
|
rna-seq
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
|
|
rubygem-bio-shell
|
|
|
|
salmon
|
*/*: bump consumers after devel/boost* update
|
2024-10-03 13:25:14 +03:00 |
|
sam2pairwise
|
|
|
|
samtools
|
|
|
|
scrm
|
|
|
|
seaview
|
|
|
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan3
|
|
|
|
seqan-apps
|
|
|
|
seqkit
|
all: Bump after lang/go121 update
|
2024-08-09 06:24:08 +00:00 |
|
seqtk
|
|
|
|
seqwish
|
|
|
|
sigviewer
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
|
|
|
spoa
|
|
|
|
sra-tools
|
|
|
|
stacks
|
biology/stacks: Unbreak build on aarch64
|
2024-05-28 16:17:25 -05:00 |
|
star
|
|
|
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
all: Bump after lang/go121 update
|
2024-08-09 06:24:08 +00:00 |
|
treekin
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ucsc-userapps
|
|
|
|
ugene
|
|
|
|
unikmer
|
all: Bump after lang/go121 update
|
2024-08-09 06:24:08 +00:00 |
|
vcf2hap
|
|
|
|
vcf-split
|
|
|
|
vcflib
|
|
|
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
|
|
|
vsearch
|
|
|
|
vt
|
|
|
|
wfa2-lib
|
biology/wfa2-lib: fix build without libomp
|
2024-08-04 14:00:47 +02:00 |
|
wise
|
all: drop support for expired FreeBSD 14.0
|
2024-10-01 20:56:20 +02:00 |
|
Makefile
|
biology/coverm: New port: Read coverage calculator for metagenomics
|
2024-10-04 20:09:27 -07:00 |
