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ports/biology
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Jason W. Bacon be3bc42e2e biology/vsearch: Update to 2.30.2 
Allow a UDB file to be written to a pipe or stdout
Correct computation of median cluster size after dereplication
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
2025-12-18 13:12:16 -06:00
..
abyss
Mk/bsd.commands.mk: Use absolute path to define GMAKE
2024-12-29 12:34:56 +01:00
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
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
atac-seq
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
augustus
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
avida
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
2023-12-31 01:37:05 +01:00
babel
…
bamtools
biology/bamtools: Update to 2.5.3
2025-05-19 16:21:57 -05:00
bamutil
…
barrnap
…
bbmap
biology/bbmap: Update to 39.34
2025-08-21 15:31:40 -05:00
bcf-score
*/*: chase the upgrade to SuiteSparse
2025-08-01 23:08:37 +02:00
bcftools
biology/bcftools: Update to 1.22
2025-06-04 08:26:12 -05:00
bedtools
biology/bedtools: Update to 2.31.1
2023-11-08 10:42:09 -06:00
bfc
…
bifrost
biology/bifrost: Remove USE_GCC, fix build with clang19
2025-05-27 09:08:27 -05:00
bio-mocha
biology/bio-mocha: Use latest versions of htslib and bcftools
2025-06-21 17:08:50 -05:00
bioawk
…
biococoa
GNUstep: Bump dependent PORTREVISION
2025-08-12 08:03:53 -03:00
biolibc
biology/biolibc: Update to 0.2.7
2025-04-26 15:35:36 -05:00
biolibc-tools
biology/biolibc-tools: Update to 0.1.5
2025-04-26 15:40:24 -05:00
bioparser
…
biosig
*/*: chase the upgrade to SuiteSparse
2025-08-01 23:08:37 +02:00
biosoup
…
biostar-tools
biology/biostar-tools: Update to 2.1
2025-12-18 08:40:26 -06:00
bolt-lmm
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
bowtie
…
bowtie2
biology/bowtie2: Update to 2.5.4
2024-05-24 06:33:53 -05:00
btllib
devel/sdsl-lite: update 2.1.1-137 → 2.3.1.v.20
2025-10-10 01:08:05 -07:00
bwa
*/*: Älven's ports to use FreeBSD.org email
2025-07-29 01:38:52 +04:00
canu
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
cd-hit
…
cdbfasta
…
chip-seq
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
clustal-omega
…
clustalw
…
coverm
lang/rust: Bump revisions after 1.92.0
2025-12-16 13:12:31 +01:00
cufflinks
biology/cufflinks: fix build with Boost-1.89 (+)
2025-10-22 03:04:20 +03:00
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
biology/diamond: Update to 2.1.16 and add test target
2025-11-29 10:24:36 -04:00
dsr-pdb
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
edlib
…
emboss
*/*: Refactor with IGNORE_WITH_MYSQL
2023-12-29 19:24:39 +01:00
erminej
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
exonerate
biology/exonerate: remove maintainer (email address gone)
2024-10-28 13:41:54 +01:00
fasda
biology/fasda: Update to 0.2.0.1
2025-05-25 09:26:46 -05:00
fasda-utils
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
fasta
MAN[1-5]PREFIX: eleminate its usage and move man to share/man
2024-01-09 16:41:04 +01:00
fasta3
MAN?PREFIX: eleminate its usage and move man to share/man
2024-01-10 09:16:01 +01:00
fastahack
…
fastani
biology/fastani: Broken where OpenMP isn't available; Update WWW
2024-11-02 23:47:52 -07:00
fastdnaml
…
fastool
…
fastp
biology/fastp: Update to 0.26.0
2025-06-07 07:28:25 -05:00
fastq-trim
biology/fastq-trim: Update to 0.1.4
2025-04-30 06:11:14 -05:00
fastqc
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
fasttree
biology/fasttree: Update to 2.1.11
2024-12-03 08:55:06 -06:00
fastx-toolkit
…
fermi-lite
biology/fermi-lite: enable on powerpc64le
2025-01-29 17:56:29 +01:00
figtree
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
flash
…
fluctuate
…
freebayes
biology/freebayes: Update to 1.3.9
2025-02-18 14:45:11 -06:00
garlic
…
gatk
biology/gatk: update 4.6.1.0 → 4.6.2.0
2025-08-27 10:24:54 -07:00
gcta
*/*: bump PORTREVISION after OpenBLAS upgrade
2025-01-28 17:42:55 +01:00
gemma
*/*: bump PORTREVISION after OpenBLAS upgrade
2025-01-28 17:42:55 +01:00
generand
biology/generand: Move man pages to share/man
2024-03-02 19:14:06 +00:00
gff2ps
…
gffread
…
gkl
biology/gkl: update 0.8.11-9 → 0.9.1
2025-08-23 11:26:47 -07:00
gmap
…
gperiodic
gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move
2025-03-17 00:02:08 -04:00
graphlan
…
groopm
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
haplohseq
biology/haplohseq: fix build with Boost-1.89 (+)
2025-10-22 03:04:22 +03:00
hhsuite
*/*: bump PORTREVISION after OpenMPI upgrade
2024-02-18 10:29:31 +01:00
hisat2
…
hmmer
biology/hmmer: update to 3.4
2024-10-28 13:41:48 +01:00
htslib
biology/*: remove useless USES=pathfix
2025-07-23 17:07:20 +02:00
hyphy
biology/hyphy: Update to 2.5.90
2025-12-14 20:43:27 -04:00
igv
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
infernal
biology/infernal: update 1.1.4 → 1.1.5
2025-01-30 08:35:31 +01:00
iolib
biology/iolib: Moved man to share/man
2024-02-22 14:23:48 +01:00
iqtree
biology/iqtree: Update to 3.0.1
2025-12-14 23:45:01 -04:00
jalview
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
jellyfish
biology/jellyfish: Move man pages to share/man
2024-03-02 19:17:36 +00:00
kallisto
biology/kallisto: Remove USE_GCC, fix build with clang19
2025-05-27 09:19:38 -05:00
kmcp
various: Bump Go ports for 1.24.11
2025-12-03 13:24:45 -05:00
lamarc
biology/lamarc: New maintainer hayzam@alchemilla.io
2025-05-20 18:16:25 -05:00
libbigwig
biology/libbigwig: update 0.4.7 → 0.4.8
2025-01-18 01:52:23 -08:00
libcombine
libxml2: chase libxml soversion bump
2025-06-30 11:04:22 +02:00
libgff
…
libgtextutils
biology/*: remove useless USES=pathfix
2025-07-23 17:07:20 +02:00
libneurosim
devel/automake: Update to 1.17
2024-07-20 13:27:02 +02:00
libnuml
libxml2: chase libxml soversion bump
2025-06-30 11:04:22 +02:00
libsbml
biology/*: remove useless USES=pathfix
2025-07-23 17:07:20 +02:00
libsedml
libxml2: chase libxml soversion bump
2025-06-30 11:04:22 +02:00
linux-foldingathome
biology/linux-foldingathome: Fix WRKSRC paths
2025-09-03 14:30:55 +02:00
locarna
biology/locarna: Move man pages to share/man
2024-03-03 10:04:08 +00:00
mafft
biology/mafft: Moved man to share/man
2024-02-22 14:23:49 +01:00
mapm3
…
mashmap
biology/mashmap: Broken on armv7
2024-01-12 17:57:41 -08:00
mca-calling
biology/mca-calling: Core tools for mCA event calling
2024-10-24 08:32:05 -05:00
megahit
biology/megahit: Update to 1.2.9.20
2025-05-23 07:33:33 -05:00
metaeuk
biology/metaeuk: builds now fine on powerpc64le
2025-01-29 17:56:26 +01:00
migrate
biology/migrate: fix build on !x86
2024-07-09 12:04:31 +02:00
minimap2
biology/minimap2: Remove extraneous file that snuck in the last commit
2025-06-21 16:47:09 -05:00
mmseqs2
biology/mmseqs2: Update to 17.b804.f
2025-01-25 07:24:31 -06:00
molden
biology/molden: Take maintainership
2025-11-05 07:30:24 -08:00
mothur
biology/mothur: update 1.48.1 → 1.48.2
2024-11-04 23:25:49 -08:00
mrbayes
…
mummer
biology/mummer: update 4.0.0 → 4.0.1
2025-02-08 00:07:06 -08:00
muscle
…
ncbi-blast+
biology/ncbi-blast+: Update to 2.17.0
2025-07-24 16:05:11 -05:00
ncbi-cxx-toolkit
biology/ncbi-cxx-toolkit: update 29.6.0 → 29.7.0
2025-11-03 23:21:32 -08:00
ncbi-entrez-direct
various: Bump Go ports for 1.24.11
2025-12-03 13:24:45 -05:00
ncbi-toolkit
all: drop support for expired FreeBSD 14.0
2024-10-01 20:56:20 +02:00
ngs-sdk
biology/ngs-sdk: Attempt to fix build on i386
2024-04-28 00:10:02 -07:00
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
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8
2023-12-25 16:59:52 +08:00
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
perl@: adopt a few ports
2025-05-28 10:28:10 +02:00
paml
biology/paml: Update to 4.10.9
2025-05-14 12:59:29 -03:00
pbbam
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
peak-classifier
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
pear-merger
MANPREFIX: eliminate its usage
2024-01-12 16:11:29 +01:00
phrap
…
phred
…
phyml
biology/phyml: fix build on non-amd64
2024-06-16 17:25:18 +02:00
picard-tools
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
plink
biology/plink: enable on powerpc64le by using SSE translation
2025-08-13 17:33:19 +02:00
pooler
biology/pooler: Update to 1.89
2025-02-01 01:36:31 +00:00
preseq
preseq: Not for 32-bit platforms
2024-11-24 07:50:11 -06:00
primer3
…
prodigal
…
prodigy-lig
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
protomol
graphics/tiff: Update to 4.6.0
2024-04-27 14:44:59 +02:00
psi88
biology/psi88: Fix building with Flang
2025-12-10 19:14:40 +03:00
py-bcbio-gff
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-biom-format
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-biopython
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-biosig
python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc
2025-06-19 16:28:47 -04:00
py-bx-python
biology/py-bx-python: update 0.13.0 → 0.14.0
2025-08-24 20:30:53 -07:00
py-crossmap
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-cutadapt
biology/py-cutadapt: update to 5.2
2025-10-29 08:41:05 +01:00
py-deeptools
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-deeptoolsintervals
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-dna-features-viewer
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-dnaio
biology/py-dnaio: Update to 1.2.4
2025-10-22 07:25:06 +00:00
py-ete3
*/*: switch dependency from devel/py-lxml5 to devel/py-lxml
2025-09-15 22:55:40 +09:00
py-Genesis-PyAPI
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-gffutils
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-goatools
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-gtfparse
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-hits
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-htseq
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-libnuml
biology/{,py-}libnuml: update 1.1.6 → 1.1.7
2025-03-28 02:54:11 -07:00
py-libsedml
biology/{,py-}libsedml: update 2.0.32 → 2.0.33
2025-04-24 00:33:39 -07:00
py-loompy
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-macs2
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-macs3
Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
2025-04-09 22:55:11 +08:00
py-mrcfile
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-multiqc
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-newick
biology/py-newick: Update to 1.10.0
2025-03-22 13:41:03 +00:00
py-ont-fast5-api
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-pandas-charm
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-py2bit
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-pybigwig
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-pydeseq2
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-pyfaidx
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-pyrodigal
python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc
2025-06-19 16:28:47 -04:00
py-pysam
python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc
2025-06-19 16:28:47 -04:00
py-PySCeS
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-python-libsbml
python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc
2025-06-19 16:28:47 -04:00
py-pywgsim
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-resdk
biology/py-resdk: update 21.2.1 → 22.0.0
2025-04-02 02:10:43 -07:00
py-scikit-bio
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
py-valerius
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-xenaPython
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
pyfasta
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
python-nexus
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
R-cran-Biobase
biology/R-cran-Biobase: Update to 2.66.0
2025-04-11 14:28:35 +00:00
R-cran-BiocGenerics
biology/R-cran-BiocGenerics: Update to 0.52.0
2025-04-11 14:28:35 +00:00
R-cran-BiocManager
biology/R-cran-BiocManager: Update to 1.30.27
2025-12-18 06:21:31 -06:00
rainbow
…
rampler
…
readseq
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
rna-seq
all: bump PORTREVISION after updating graphics/libyuv
2025-08-31 12:30:51 +02:00
ruby-bio
…
rubygem-bio
biology/rubygem-bio: Update to 2.0.6
2025-03-19 11:46:26 +08:00
rubygem-bio-executables
…
rubygem-bio-old-biofetch-emulator
…
rubygem-bio-shell
…
salmon
*: WITH_DEBUG is a user feature not a port one
2025-12-18 15:58:08 +01:00
sam2pairwise
…
samtools
biology/samtools: Update to 1.22
2025-06-04 08:26:12 -05:00
scrm
biology/scrm: Move man pages to share/man
2024-03-02 19:59:23 +00:00
seaview
biology/seaview: Update version 5.0.5=>5.1
2025-03-26 08:36:45 +01:00
seqan
…
seqan1
…
seqan3
biology/seqan3: update 3.3.0 → 3.4.0
2025-08-28 12:28:16 -07:00
seqan-apps
…
seqkit
many: Unpin Go ports
2025-12-16 00:06:00 +01:00
seqtk
biology/seqtk: Update to 1.5
2025-06-04 09:20:45 -05:00
seqwish
biology/seqwish: Unbundle sdsl-lite and fix some clang19 compilation errors
2025-10-10 20:49:16 -07:00
sigviewer
…
slclust
…
smithwaterman
…
snpeff
biology/snpeff: Mark BROKEN and set expiration date to 2026-01-31
2025-12-07 20:52:10 +01:00
spoa
biology/spoa: update 4.1.0 → 4.1.5
2025-11-04 22:57:34 -08:00
sra-tools
biology/sra-tools: Update to 3.3.0
2025-12-17 10:18:23 -06:00
stacks
biology/stacks: fix build without libomp
2025-01-22 12:27:04 +01:00
star
biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
2024-05-05 09:58:47 -05:00
stringtie
…
subread
biology/subread: Update to 2.1.0
2025-03-27 17:05:26 -05:00
tabixpp
biology/tabixpp: Undeprecate and update to 1.1.2
2025-02-18 09:39:35 -06:00
taxonkit
various: Bump Go ports for 1.24.11
2025-12-03 13:24:45 -05:00
treekin
*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS
2025-01-24 13:18:28 +01:00
treepuzzle
…
trimadap
biology/trimadap: drop not necessary powerpc64le knob
2025-01-29 17:56:25 +01:00
trimmomatic
Mk/**java.mk: Convert bsd.java.mk to USES
2024-12-31 09:57:55 +01:00
tRNAscan-SE
…
ucsc-userapps
biology/ucsc-userapps: Update to v474
2024-11-28 09:59:20 -06:00
ugene
MAN?PREFIX: eleminate its usage and move man to share/man
2024-01-10 09:16:01 +01:00
unikmer
various: Bump Go ports for 1.24.11
2025-12-03 13:24:45 -05:00
vcf2hap
biology/vcf2hap: Move man pages to share/man
2024-03-02 20:07:47 +00:00
vcf-split
biology/vcf-split: Move man pages to share/man
2024-03-02 20:04:57 +00:00
vcflib
biology/vcflib: update BUILD_DEPENDS to keep building with zig 0.14
2025-12-18 11:48:02 +01:00
vcftools
biology/vcftools: Update to 0.1.17
2025-05-15 07:26:46 -05:00
velvet
…
viennarna
biology/viennarna: Unbundle dlib, use port dependency instead
2025-10-09 07:58:45 -07:00
vsearch
biology/vsearch: Update to 2.30.2
2025-12-18 13:12:16 -06:00
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/py-orange3-bioinformatics: Remove expired port
2025-06-23 21:01:46 +02:00