Jason W. Bacon 481ae0481b biology/biolibc: Update to 0.2.4.3 ... Add extern "C" to support use from C++ apps		2023-06-10 07:15:29 -05:00
..
abyss	biology/abyss: Fix build with llvm15	2023-06-07 09:25:09 +02:00
ad2vcf
artemis
atac-seq	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
augustus	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
avida
babel
bamtools
bamutil
barrnap
bbmap
bcf-score	biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics	2023-02-25 08:27:46 -06:00
bcftools	biology/bcftools: Update to 1.17	2023-02-24 17:30:58 -06:00
bedtools	biology/bedtools: Update to 2.31.0	2023-04-28 20:03:07 -05:00
bfc
bio-mocha
bioawk
biococoa	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
biolibc	biology/biolibc: Update to 0.2.4.3	2023-06-10 07:15:29 -05:00
biolibc-tools	biology/biolibc-tools: Update to 0.1.4.6	2023-06-10 06:57:56 -05:00
bioparser
biosig	*/*: llvm15 build fixes	2023-05-17 18:30:15 +02:00
biosoup	biology/biosoup: Update 0.10.0-2 → 0.11.0	2023-05-19 00:54:16 -07:00
biostar-tools	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
bolt-lmm	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
bowtie
bowtie2
bwa
canu	*/*: Refactor java/openjdk7 removal	2023-04-04 13:10:53 -05:00
cd-hit
cdbfasta
checkm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
clustal-omega
clustalw
cufflinks	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
cytoscape
ddocent	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
diamond	biology/diamond: Update to 2.1.6	2023-03-18 12:49:03 -03:00
dsr-pdb	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
edlib
emboss
erminej
exonerate
fasda	biology/fasda: Update to 0.1.3	2023-06-10 06:57:56 -05:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Update to 0.23.4	2023-05-31 10:40:00 -05:00
fastq-trim
fastqc	biology/fastqc: Update to 0.12.1	2023-03-04 18:17:20 -06:00
fasttree
fastx-toolkit	biology/fastx-toolkit: Unbreak build on 14-CURRENT	2023-03-07 11:28:13 -06:00
figtree
flash
fluctuate
freebayes
garlic
gatk	biology/gatk: Update 4.3.0.0 → 4.4.0.0	2023-06-04 15:02:58 -07:00
gcta	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
gemma	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
generand
gff2ps	biology/gff2ps: drop maintainership	2023-05-21 16:20:36 +00:00
gffread
gmap
gperiodic	accessibility/at-spi2-core: update to 2.46.0	2023-03-02 06:23:10 +01:00
graphlan
groopm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
haplohseq	*/*: bump all direct Boost cunsumers	2023-04-27 21:25:55 +03:00
hhsuite	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
hisat2
hmmer
htslib	biology/htslib: fix build on armv7	2023-04-18 23:55:29 +02:00
hyphy	biology/hyphy: Update to 2.5.51hf	2023-05-28 21:09:56 -03:00
igv	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
infernal
iolib
iqtree	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
jalview
jellyfish
kallisto	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
kmcp	biology/kmcp: Update 0.9.1 → 0.9.2	2023-05-21 23:54:53 -07:00
lamarc
libbigwig
libcombine	biology/libcombine: Fix build with libsbml 5.20.0	2023-05-27 12:24:05 +08:00
libgff
libgtextutils
libneurosim
libnuml
libsbml	biology/libsbml: Update to 5.20.0	2023-05-27 12:07:11 +08:00
libsedml	biology/libsedml: Fix build with libsbml 5.20.0	2023-05-27 12:24:05 +08:00
linux-foldingathome
mafft
mapm3
megahit
metaeuk
migrate
minimap2	biology/minimap2: Update to 2.25	2023-04-29 09:53:40 -05:00
mmseqs2
molden	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
mothur
mrbayes
mummer
muscle
ncbi-blast+	biology/ncbi-blast+: Tag only for 64-bit architectures	2023-05-29 08:59:01 -05:00
ncbi-cxx-toolkit	graphics/proj: Update to 9.2.0	2023-03-09 13:42:31 +01:00
ncbi-entrez-direct	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
ncbi-toolkit	biology/ncbi-toolkit: Fix build with llvm15	2023-06-06 22:45:25 +02:00
ncbi-vdb	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
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
p5-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbseqan
peak-classifier	biology/peak-classifier: Update to 0.1.4.8	2023-06-10 06:57:56 -05:00
pear-merger
phrap
phred
phyml	biology/phyml: fix build on non-x86	2023-05-08 10:25:50 +02:00
picard-tools	*/*: Refactor java/openjdk7 removal	2023-04-04 13:10:53 -05:00
plink	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
pooler
primer3
prodigal
prodigy-lig	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
protomol
psi88	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-bcbio-gff	biology/py-bcbio-gff: Update to 0.7.0	2023-03-16 17:32:06 -05:00
py-biom-format	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-biopython	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-biosig	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-bx-python	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-crossmap	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-cutadapt
py-deeptools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-deeptoolsintervals
py-dna-features-viewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-dnaio
py-ete3	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: Update 0.11.0 → 0.11.1	2023-03-12 01:02:31 -08:00
py-goatools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-gtfparse	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-hits
py-libnuml	biology/py-libnuml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-libsedml	biology/py-libsedml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-loompy	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-macs2	biology/py-macs2: Update to 2.2.8	2023-05-22 12:14:04 -05:00
py-mrcfile	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-multiqc	biology/py-multiqc: Update to 1.14	2023-05-12 07:55:38 -05:00
py-ont-fast5-api	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-orange3-bioinformatics	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-orange3-single-cell	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
py-pandas-charm	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-py2bit
py-pybigwig	biology/py-pybigwig: Update to 0.3.21	2023-04-01 16:10:15 -05:00
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: Update 2.0.3 → 2.1.0	2023-03-19 09:42:53 -07:00
py-pysam	biology/py-pysam: unbundle biology/htslib	2023-05-25 11:39:33 +02:00
py-PySCeS	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-python-libsbml
py-pywgsim
py-resdk	biology/py-resdk: Update 16.0.0 → 17.0.0	2023-04-27 01:36:47 -07:00
py-scikit-bio	www/py-cachecontrol: Fix port	2023-05-08 07:55:57 +08:00
py-valerius
py-xenaPython
pyfasta	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
python-nexus
rainbow
rampler	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
readseq
recombine
rna-seq	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
sam2pairwise
samtools	biology/samtools: Update to 1.17	2023-02-24 17:27:21 -06:00
scrm
seaview
seqan
seqan1
seqan3	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
seqan-apps
seqio
seqkit	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
seqtk	biology/seqtk: Update to 1.4	2023-05-23 17:42:13 -05:00
sigviewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
sim4
slclust
smithwaterman
snpeff
spoa	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
sra-tools	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: Update 0.14.1 → 0.14.2	2023-04-14 22:02:19 -07:00
treekin	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene
unikmer	all: Bump PORTREVISION after lang/go{119,120} update	2023-04-08 10:13:25 -05:00
vcf2hap
vcf-split
vcflib
vcftools
velvet
viennarna
vsearch
vt
wfa2-lib	*/*: Sunset 12.3-RELEASE from ports tree	2023-03-30 18:59:51 -05:00
wise	*/*: llvm15 build fixes	2023-05-17 18:30:15 +02:00
Makefile	biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics	2023-02-25 08:27:46 -06:00