Jason W. Bacon 84399cefee biology/vsearch: Update to 2.30.0 ... Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate Changes: https://github.com/torognes/vsearch/releases Reported by: portscout		2025-03-02 06:37:09 -06:00
..
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
abyss	Mk/bsd.commands.mk: Use absolute path to define GMAKE	2024-12-29 12:34:56 +01:00
ad2vcf	…
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: remove support for expired FreeBSD 13.3	2025-01-01 17:09:59 +01:00
augustus	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
avida	…
babel	…
bamtools	*/*: Bump dependencioes after devel/jsoncpp update	2024-09-12 09:20:06 -07:00
bamutil	…
barrnap	…
bbmap	biology/bbmap: Update to 39.15	2025-01-16 06:35:49 -06:00
bcf-score	*/*: bump PORTREVISION after the upgrade to Suitesparse	2025-01-11 11:02:35 +01:00
bcftools	biology/bcftools: Update to 1.21	2024-10-09 17:23:09 -05:00
bedtools	…
bfc	…
bifrost	biology/bifrost: Update to 1.3.5	2024-03-18 09:29:43 -05:00
bio-mocha	biology/bio-mocha: Update to 1.20	2024-10-09 17:23:10 -05:00
bioawk	…
biococoa	…
biolibc	…
biolibc-tools	…
bioparser	…
biosig	*/*: bump PORTREVISION after the upgrade to Suitesparse	2025-01-11 11:02:35 +01:00
biosoup	…
biostar-tools	biology/biostar-tools: Update to 2.0	2024-11-07 18:44:28 -06:00
bolt-lmm	*/*: Bump PORTREVISION after math/nlopt update	2025-03-01 16:09:11 +01:00
bowtie	…
bowtie2	…
btllib	biology/btllib: update 1.7.3 → 1.7.5	2024-12-05 10:11:11 -08:00
bwa	biology/bwa: small improvements	2025-01-06 17:29:54 +01:00
canu	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
cd-hit	…
cdbfasta	…
checkm	biology/checkm: update 1.2.2 → 1.2.3	2024-12-14 22:50:29 -08:00
chip-seq	…
clustal-omega	…
clustalw	…
coverm	lang/rust: Bump revisions after 1.85.0	2025-02-24 08:55:52 +01:00
cufflinks	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +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 2.1.11	2025-01-25 10:35:27 -04:00
dsr-pdb	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
edlib	…
emboss	…
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	…
fasta	…
fasta3	…
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 0.24.0	2024-11-16 07:10:58 -06:00
fastq-trim	…
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 WWW	2025-02-14 02:30:52 -08:00
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	…
gff2ps	…
gffread	…
gkl	Mk/**java.mk: Convert bsd.java.mk to USES	2024-12-31 09:57:55 +01:00
gmap	…
gperiodic	…
graphlan	…
groopm	…
haplohseq	biology/haplohseq: mark as BROKEN with Boost>=1.87 (+)	2025-02-14 06:17:11 +03:00
hhsuite	…
hisat2	…
hmmer	biology/hmmer: update to 3.4	2024-10-28 13:41:48 +01:00
htslib	biology/htslib: Update to 1.21	2024-10-09 17:23:08 -05:00
hyphy	biology/hyphy: Update to 2.5.69	2025-03-01 23:52:07 -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	…
iqtree	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
jalview	Mk/**java.mk: Convert bsd.java.mk to USES	2024-12-31 09:57:55 +01:00
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	biology/libbigwig: update 0.4.7 → 0.4.8	2025-01-18 01:52:23 -08:00
libcombine	…
libgff	…
libgtextutils	…
libneurosim	devel/automake: Update to 1.17	2024-07-20 13:27:02 +02:00
libnuml	…
libsbml	textproc/xerces-c3: Update to 3.3.0	2024-10-25 23:56:41 +08:00
libsedml	…
linux-foldingathome	biology/linux-foldingathome: Update to 8.4.9.	2025-02-14 09:21:35 +01:00
locarna	…
mafft	…
mapm3	…
mashmap	…
mca-calling	biology/mca-calling: Core tools for mCA event calling	2024-10-24 08:32:05 -05:00
megahit	…
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: Add NOT_FOR_ARCHS for most 32-bit processors	2024-07-20 14:55:08 -05:00
mmseqs2	biology/mmseqs2: Update to 17.b804.f	2025-01-25 07:24:31 -06:00
molden	all: return jmd's ports to the pool after safekeeping their commit bit.	2024-11-28 17:10:52 +01:00
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+	devel/grpc: Update to 1.70.1	2025-02-08 05:34:57 +08:00
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	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
ngs-sdk	…
p5-AcePerl	…
p5-Bio-ASN1-EntrezGene	…
p5-Bio-Cluster	…
p5-Bio-Coordinate	…
p5-Bio-DB-EMBL	…
p5-Bio-DB-NCBIHelper	…
p5-Bio-Das	…
p5-Bio-Das-Lite	…
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	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-BioPerl	…
p5-BioPerl-Run	…
p5-TrimGalore	biology/p5-TrimGalore: Update to 0.6.10	2024-07-23 11:01:28 -04:00
p5-transdecoder	…
paml	…
pbbam	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
peak-classifier	…
pear-merger	…
phrap	…
phred	…
phyml	…
picard-tools	Mk/**java.mk: Convert bsd.java.mk to USES	2024-12-31 09:57:55 +01:00
plink	*/*: bump PORTREVISION after OpenBLAS upgrade	2025-01-28 17:42:55 +01:00
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	biology/prodigy-lig: update 1.1.2 → 1.1.3	2024-10-15 08:33:52 -07:00
protomol	…
psi88	…
py-Genesis-PyAPI	…
py-PySCeS	biology/py-PySCeS: update 1.2.1 → 1.2.2	2024-08-03 01:27:31 -07:00
py-bcbio-gff	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
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 1.83 => 1.85	2025-02-15 20:08:17 +03:00
py-biosig	biology/{.py-}biosig: update 2.6.0 → 2.6.1	2024-08-05 07:37:01 -07:00
py-bx-python	biology/py-bx-python: update 0.11.0 → 0.13.0	2024-12-15 06:55:17 -08:00
py-crossmap	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-cutadapt	biology/py-cutadapt: Update to 5.0	2025-01-10 16:35:23 +01:00
py-deeptools	…
py-deeptoolsintervals	…
py-dna-features-viewer	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-dnaio	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-ete3	…
py-gffutils	…
py-goatools	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-gtfparse	biology/py-gtfparse: Fix fetch	2024-12-05 19:44:23 -08:00
py-hits	…
py-htseq	py-htseq: New maintainer	2024-11-28 06:22:44 -06:00
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	biology/py-multiqc: Add missing py-natsort RUN_DEPEND	2024-12-12 08:52:37 -06:00
py-newick	…
py-ont-fast5-api	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-orange3-bioinformatics	biology/py-orange3-bioinformatics: Update 4.3.1 → 4.8.4	2025-02-18 22:45:18 +03:00
py-orange3-single-cell	…
py-pandas-charm	…
py-py2bit	…
py-pybigwig	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-pyfaidx	…
py-pyrodigal	biology/py-pyrodigal: update 3.5.2 → 3.6.3	2024-11-12 00:32:35 -08:00
py-pysam	biology/py-pysam: update 0.22.1 → 0.23.0	2025-02-06 07:05:43 -08:00
py-python-libsbml	biology/py-python-libsbml: update 5.20.1 → 5.20.4	2024-11-12 02:18:13 -08:00
py-pywgsim	Multiple biology ports: Replace pypi homepage with github	2025-02-21 07:04:08 -06:00
py-resdk	biology/py-resdk: update 21.2.0 → 21.2.1	2024-11-10 19:54:22 -08:00
py-scikit-bio	biology/py-scikit-bio: update 0.6.2 → 0.6.3	2025-01-13 19:26:05 -08:00
py-valerius	…
py-xenaPython	…
pyfasta	…
python-nexus	…
rainbow	…
rampler	…
readseq	Mk/**java.mk: Convert bsd.java.mk to USES	2024-12-31 09:57:55 +01:00
rna-seq	biology/rna-seq: Add biology/star dep to metaport	2023-07-31 09:36:06 -05:00
ruby-bio	…
rubygem-bio	…
rubygem-bio-executables	…
rubygem-bio-old-biofetch-emulator	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby	2023-01-14 17:08:33 -06:00
rubygem-bio-shell	…
salmon	devel/boost: bump consumers after Boost-1.87 update	2025-02-14 06:17:22 +03:00
sam2pairwise	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
samtools	biology/samtools: Update to 1.21	2024-10-09 17:23:09 -05:00
scrm	…
seaview	biology/seaview: unbreak the port's build against FLTK 1.3.10	2025-02-05 16:37:24 +00:00
seqan	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan-apps	biology/seqan-apps: Fix build with llvm16	2023-08-06 23:53:04 +02:00
seqan1	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan3	biology/seqan3: update 3.2.0 → 3.3.0	2023-09-10 11:10:47 -07:00
seqkit	biology/seqkit: update 2.8.2 → 2.9.0	2024-11-04 17:26:42 -08:00
seqtk	…
seqwish	biology/seqwish: Set OPENMP=OFF and broken where OpenMP isn't available	2025-02-23 11:42:19 -08:00
sigviewer	…
slclust	…
smithwaterman	…
snpeff	Mk/**java.mk: Convert bsd.java.mk to USES	2024-12-31 09:57:55 +01:00
spoa	…
sra-tools	biology/sra-tools: Update to 3.2.0	2025-01-29 14:16:40 -06:00
stacks	biology/stacks: fix build without libomp	2025-01-22 12:27:04 +01:00
star	…
stringtie	…
subread	biology/subread: Update to 2.0.8	2025-01-19 06:46:51 -06:00
tRNAscan-SE	…
tabixpp	biology/tabixpp: Undeprecate and update to 1.1.2	2025-02-18 09:39:35 -06:00
taxonkit	biology/taxonkit: update 0.17.0 → 0.18.0	2024-11-04 17:26:41 -08:00
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
ucsc-userapps	biology/ucsc-userapps: Update to v474	2024-11-28 09:59:20 -06:00
ugene	…
unikmer	biology/unikmer: Update WWW	2025-01-05 20:01:04 -08:00
vcf-split	…
vcf2hap	…
vcflib	biology/vcflib: Update to 1.0.12	2024-11-25 08:49:37 -06:00
vcftools	…
velvet	…
viennarna	*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS	2025-01-24 13:18:28 +01:00
vsearch	biology/vsearch: Update to 2.30.0	2025-03-02 06:37:09 -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/ncbi-vdb: Remove expired port	2025-01-01 11:59:57 +01:00