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Jason W. Bacon 1ef610474a biology/samtools: Update to 1.24 
Numerous fixes and enhancements
Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
2026-07-11 14:32:16 -05:00
..
abyss
*/*: bump PORTREVISION after the upgrade of MPICH
2026-02-16 14:07:00 +00:00
ad2vcf
…
andi
biology/andi: update 0.14-3 → 1.15
2026-02-15 23:13:44 -08:00
artemis
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
atac-seq
biology/atac-seq: Update to 0.3.1
2026-07-03 19:39:42 -05:00
augustus
*/*: chase math/gsl update to 2.8
2026-01-29 16:16:02 +03:00
avida
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
babel
…
bamtools
biology/bamtools: Update to 2.5.3
2025-05-19 16:21:57 -05:00
bamutil
…
barrnap
biology/barrnap: update 0.9 → 1.10.6
2026-04-13 01:32:11 -07:00
bbmap
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
bcf-score
*/*: chase the upgrade to SuiteSparse
2025-08-01 23:08:37 +02:00
bcftools
biology/bcftools: Update to 1.24
2026-07-11 14:22:39 -05:00
bedtools
…
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
biology/{,py-}biosig: update 2.6.1 → 3.9.5
2026-04-18 13:58:23 -07:00
biosoup
…
biostar-tools
biology/biostar-tools: Update to 2.1
2025-12-18 08:40:26 -06:00
bolt-lmm
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2026-05-13 10:28:41 +02:00
bowtie
…
bowtie2
biology/bowtie2: Update to 2.5.5
2026-03-04 18:43:26 -06:00
btllib
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
bwa
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
canu
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
cd-hit
…
cdbfasta
…
chip-seq
biology/chip-seq: Update to 0.3.1
2026-07-03 19:42:57 -05:00
clustal-omega
…
clustalw
…
coverm
biology/coverm: update 0.7.0 → 0.8.0
2026-07-08 01:15:48 -07:00
cufflinks
biology/cufflinks: fix build with Boost-1.89 (+)
2025-10-22 03:04:20 +03:00
cytoscape
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
ddocent
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
diamond
biology/diamond: Update to 2.2.2
2026-06-24 15:46:33 -03:00
dsr-pdb
devel/boost: bump consumers after boost upgrade (+)
2025-10-20 14:48:39 +03:00
edlib
…
emboss
…
erminej
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
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
…
fasta3
…
fastahack
…
fastani
*/*: chase math/gsl update to 2.8
2026-01-29 16:16:02 +03:00
fastdnaml
…
fastool
…
fastp
biology/fastp: Update to 1.2.0
2026-03-22 07:55:42 -05:00
fastq-trim
biology/fastq-trim: Update to 0.1.4
2025-04-30 06:11:14 -05:00
fastqc
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
fasttree
biology/fasttree: Update to 2.1.11
2024-12-03 08:55:06 -06:00
fastx-toolkit
…
fermi-lite
*/*: bump PORTREVISION following devel/sse2neon update
2025-12-28 16:12:09 +01:00
figtree
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
flash
…
fluctuate
…
freebayes
biology/freebayes: Update to 1.3.9
2025-02-18 14:45:11 -06:00
garlic
…
gatk
*/*: Use C.UTF-8 locale
2026-06-30 22:03:57 +02:00
gcta
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2026-05-13 10:28:41 +02:00
gemma
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2026-05-13 10:28:41 +02:00
generand
…
gff2ps
…
gffread
biology/gffread: Update to 0.12.9
2026-04-13 08:20:48 -05:00
gkl
*/*: bump portrevision for openjdk dependency change
2026-04-08 09:11:51 +02:00
gmap
…
gperiodic
gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move
2025-03-17 00:02:08 -04:00
graphlan
…
groopm
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
haplohseq
biology/haplohseq: fix build with Boost-1.89 (+)
2025-10-22 03:04:22 +03:00
hhsuite
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
hisat2
biology/hisat2: Update to 2.2.2
2026-02-01 11:22:21 -06:00
hmmer
biology/hmmer: update to 3.4
2024-10-28 13:41:48 +01:00
htslib
biology/htslib: Update to 1.24
2026-07-11 14:21:04 -05:00
hyphy
biology/hyphy: Update to 2.5.101
2026-06-24 15:55:08 -03:00
igv
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
infernal
biology/infernal: not for ppc64le
2026-02-24 01:44:47 +01:00
iolib
biology/iolib: fix build on armv7
2026-03-24 20:12:38 +01:00
iqtree
biology/iqtree: Update to 3.1.3
2026-06-24 15:46:33 -03:00
jalview
*/*: Use C.UTF-8 locale
2026-06-30 22:03:57 +02:00
jellyfish
…
kallisto
biology/kallisto: Update to 0.52.0,1
2026-03-04 17:28:49 -06:00
kmcp
various: Bump go ports for go-1.25.12 / 1.26.5
2026-07-10 09:54:15 +02:00
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
biology/libgff: Update to 2.0.1
2026-03-07 13:06:00 -06:00
libgtextutils
biology/*: remove useless USES=pathfix
2025-07-23 17:07:20 +02:00
libneurosim
misc: fix build with python 3.12
2026-02-15 07:51:06 +00:00
libnuml
libxml2: chase libxml soversion bump
2025-06-30 11:04:22 +02:00
libsbml
biology/libsbml: Remove unnecessary substitution
2026-06-27 04:43:54 +08:00
libsedml
libxml2: chase libxml soversion bump
2025-06-30 11:04:22 +02:00
linux-foldingathome
biology/linux-foldingathome: Update license
2026-06-09 16:58:33 +02:00
locarna
biology/locarna: update 2.0.0 → 2.0.1
2026-05-05 23:54:37 -07:00
mafft
…
mapm3
…
mashmap
*/*: chase math/gsl update to 2.8
2026-01-29 16:16:02 +03:00
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
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
migrate
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
minimap2
biology/minimap2: Update to 2.31
2026-05-20 07:16:44 -05:00
mmseqs2
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
molden
biology/molden: Take maintainership
2025-11-05 07:30:24 -08:00
mothur
biology/mothur: Fix build on 16
2026-06-04 18:03:25 -07:00
mrbayes
…
mummer
biology/mummer: update 4.0.0 → 4.0.1
2025-02-08 00:07:06 -08:00
muscle
…
ncbi-blast+
databases/lmdb0: Add port for LMDB 0.9.x legacy ABI
2026-07-06 08:57:32 -07:00
ncbi-cxx-toolkit
databases/lmdb0: Add port for LMDB 0.9.x legacy ABI
2026-07-06 08:57:32 -07:00
ncbi-entrez-direct
various: Bump go ports for go-1.25.12 / 1.26.5
2026-07-10 09:54:15 +02:00
ncbi-toolkit
biology/ncbi-toolkit: Unbreak by fixing chained C comparison in tools/readdb.c
2026-07-10 18:00:13 -07:00
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
biology/iolib: Update 1.14.10 => 1.15.1, take maintainership
2026-01-20 16:51:34 +04:00
p5-Bio-Variation
…
p5-BioPerl
…
p5-BioPerl-Run
…
p5-transdecoder
…
paml
biology/paml: Update to 4.10.10
2026-02-19 12:08:51 -04:00
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
…
phrap
…
phred
…
phyml
…
picard-tools
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
plink
*/*: bump PORTREVISION after the upgrade of OpenBLAS
2026-05-13 10:28:41 +02:00
pooler
biology/pooler: Update to 1.89
2025-02-01 01:36:31 +00:00
preseq
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
primer3
…
prodigal
…
prodigy-lig
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
protomol
…
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
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-biopython
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-biosig
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-bx-python
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
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
biology/py-deeptools: Update to 3.5.6
2026-04-27 10:35:51 -05:00
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
Mk/Uses/python.mk: Remove USE_PYTHON=cython3{,_run,_test}
2026-01-16 01:22:12 +08:00
py-ete3
*: Fix spelling and typos in comments and pkg-descr's of various ports
2026-05-24 19:45:05 +03:00
py-Genesis-PyAPI
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-gffutils
biology/py-gffutils: update 0.13 → 0.14
2026-04-01 23:45:22 -07:00
py-goatools
biology/py-goatools: Fix build with python 3.12
2026-07-03 19:36:51 -05:00
py-gtfparse
biology/py-gtfparse: update 2.7.1 → 2.8.0
2026-07-09 00:23:13 -07:00
py-hits
biology/py-hits: update 0.1 → 0.5.1
2026-05-29 19:32:42 -07:00
py-htseq
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
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
biology/py-loompy: update 3.0.7 → 3.0.8
2026-06-08 12:50:40 -07:00
py-macs2
all: schedule for removal on 2026-09-15 for lang/cython0
2026-07-02 22:19:17 +02:00
py-macs3
biology/py-macs3: Fix USE_PYTHON=cython usage
2026-06-27 04:47:20 +08:00
py-mrcfile
biology/py-mrcfile: update 1.5.3 → 1.5.4
2026-06-08 12:50:40 -07:00
py-multiqc
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-newick
biology/py-newick: Update to 1.11.0
2026-02-04 01:17:26 +00:00
py-ont-fast5-api
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-pandas-charm
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-py2bit
biology/py-py2bit: fix build with python different from 3.11
2026-06-12 18:47:16 +00:00
py-pybigwig
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
2025-03-07 23:05:21 -05:00
py-pydeseq2
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
py-pyfaidx
biology/py-pyfaidx: update 0.5.9.5 → 0.9.0.4
2026-06-02 15:51:16 -07:00
py-pyrodigal
biology/py-pyrodigal: update 3.6.3 → 3.7.1
2026-04-30 19:03:42 -07:00
py-pysam
biology/py-pysam: update 0.23.0 → 0.24.0
2026-04-28 00:57:01 -07:00
py-PySCeS
biology/py-PySCeS: update 1.2.2 → 1.2.3
2026-06-11 11:24:28 -07:00
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: Fix run-depends
2026-04-08 08:19:17 -07:00
py-scikit-bio
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
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
*/*: bump PORTREVISION after switching to NumPy 2.x
2026-05-05 22:29:37 +03:00
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
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
rna-seq
biology/rna-seq: Update to 0.2.0
2026-03-04 17:38:41 -06:00
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
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
sam2pairwise
…
samtools
biology/samtools: Update to 1.24
2026-07-11 14:32:16 -05:00
scrm
…
seaview
biology/seaview: Update version 5.0.5=>5.1
2025-03-26 08:36:45 +01:00
seqan
…
seqan1
…
seqan3
biology/seqan3: update 3.4.0 → 3.4.2
2026-04-14 00:12:39 -07:00
seqan-apps
…
seqkit
various: Bump go ports for go-1.25.12 / 1.26.5
2026-07-10 09:54:15 +02:00
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
misc/libxdf: update 0.991 → 1.0.1
2026-07-07 01:56:24 -07:00
slclust
…
smithwaterman
…
spoa
biology/spoa: update 4.1.0 → 4.1.5
2025-11-04 22:57:34 -08:00
sra-tools
biology/sra-tools: lib64 -> lib
2026-05-29 16:48:39 -05:00
stacks
biology/stacks: fix build without libomp
2025-01-22 12:27:04 +01:00
star
all: drop support for FreeBSD 13, mips and risc64sf
2026-05-07 23:47:29 +02:00
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 go-1.25.12 / 1.26.5
2026-07-10 09:54:15 +02:00
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
TrimGalore
biology/TrimGalore: update 2.2.0 -> 2.3.0
2026-07-10 17:43:11 +02:00
trimmomatic
*/*: bump portrevision after java_default=25 update
2026-04-02 23:06:57 +02:00
tRNAscan-SE
…
ucsc-userapps
biology/ucsc-userapps: Clean up USES=python
2026-06-27 04:47:21 +08:00
ugene
biology/ugene: fix build on aarch64
2026-04-21 22:14:30 +02:00
unikmer
various: Bump go ports for go-1.25.12 / 1.26.5
2026-07-10 09:54:15 +02:00
vcf2hap
…
vcf-split
…
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: update 2.7.0 → 2.7.2
2026-06-27 23:49:08 -07:00
vsearch
biology/vsearch: Update to 2.31.0
2026-05-03 11:24:22 -05:00
vt
…
wfa2-lib
biology/wfa2-lib: Update to 2.3.6
2026-03-23 16:42:52 -05:00
wise
all: drop support for expired FreeBSD 14.0
2024-10-01 20:56:20 +02:00
Makefile
biology/p5-TrimGalore: update 0.6.11->2.2.0 and move to biology/TrimGalore
2026-05-24 09:47:52 +02:00