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freebsd-ports/biology
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Jason W. Bacon 57d280a35e biology/minimap2: Update to 2.25 
New feature to output sequences in secondary alignments
Several minor enhancements and fixes
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout
2023-04-29 09:53:40 -05:00
..
abyss *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
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 biology/barrnap: Update descr 2022-11-24 19:12:18 -08:00
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 biology/bio-mocha: Update to 1.16 2023-01-05 17:21:03 -06:00
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 2022-12-11 14:06:23 -06:00
biolibc-tools biology/biolibc-tools: Update to 0.1.4.1 2022-12-13 18:11:56 -06:00
bioparser
biosig *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
biosoup *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
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 biology/bowtie2: Update to 2.5.1 2023-01-21 16:30:48 -06:00
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 biology/cytoscape: Broken on armv6, armv7 2022-12-10 23:41:04 -08:00
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 biology/emboss: Ignore with mysql 8.0 2023-02-01 04:39:38 -06:00
erminej
exonerate
fasda biology/fasda: Fast and simple differential analysis 2022-12-12 11:17:22 -06:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastp *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
fastq-trim biology/fastq-trim: Update to 0.1.2 2022-12-11 15:24:05 -06:00
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 biology/freebayes: Drop redundant tabixpp dep 2023-01-22 10:42:34 -06:00
garlic
gatk biology/gatk: Update 4.2.6.1 -> 4.3.0.0 2022-11-26 20:06:47 -08:00
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
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 biology/hmmer: Update to 3.3.2 2022-10-11 15:13:01 -05:00
htslib biology/htslib: fix build on armv7 2023-04-18 23:55:29 +02:00
hyphy biology/hyphy: Update to 2.5.50 2023-04-19 13:30:57 -03:00
igv audio/opus: bump consumers after update to 1.4 2023-04-25 17:17:15 +02:00
infernal biology/infernal: Update to 1.1.4 2022-10-12 11:15:54 +01:00
iolib
iqtree *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
jalview biology/jalview: Update 2.11.1.4 -> 2.11.2.5 2022-10-11 23:58:18 -07:00
jellyfish biology/jellyfish: Bump PORTREVISION for biology/htslib update 2023-01-05 19:24:44 -06:00
kallisto *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
kmcp all: Bump PORTREVISION after lang/go{119,120} update 2023-04-08 10:13:25 -05:00
lamarc biology/lamarc: Refactor after wxgtk28 removal 2022-12-31 04:54:58 +01:00
libbigwig
libcombine biology/libcombine: Update 0.2.19 -> 0.2.20 2022-12-08 03:11:24 -08:00
libgff
libgtextutils
libneurosim
libnuml
libsbml biology/libsbml: Update WWW and clean up pkg-descr 2023-04-06 01:29:43 +08:00
libsedml
linux-foldingathome
mafft
mapm3
megahit biology/megahit: Add cmake patch to respect ports build flags 2022-11-24 08:10:13 -06:00
metaeuk biology/metaeuk: Fix build on systems withour OpenMP enabled 2022-12-10 01:51:02 -08:00
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+ devel/grpc: Update to 1.54.0 (should be part of 8f17596cf5) 2023-04-20 02:53:02 +08:00
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 */*: Bump PORTREVISION for consumers of libunistring 2022-10-22 11:36:07 +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 biology/p5-transdecoder: Update to 5.7.0 2023-01-30 16:30:54 -06:00
p5-TrimGalore
paml biology/paml: Update to 4.10.6 2022-11-12 22:35:29 -04:00
pbbam biology/pbbam: Bump PORTREVISION for biology/htslib update 2023-01-05 19:25:09 -06:00
pbseqan
peak-classifier *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
pear-merger
phrap
phred
phyml
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 biology/pooler: update to 1.86 2022-12-19 08:56:15 +01:00
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 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-deeptools *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-deeptoolsintervals */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-dna-features-viewer *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-dnaio */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-ete3 audio/opus: bump consumers after update to 1.4 2023-04-25 17:17:15 +02:00
py-Genesis-PyAPI */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
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 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
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 *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-mrcfile *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-multiqc *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
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 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pybigwig biology/py-pybigwig: Update to 0.3.21 2023-04-01 16:10:15 -05:00
py-pyfaidx */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pyrodigal biology/py-pyrodigal: Update 2.0.3 → 2.1.0 2023-03-19 09:42:53 -07:00
py-pysam */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-PySCeS *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-python-libsbml */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pywgsim */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-resdk biology/py-resdk: Update 16.0.0 → 17.0.0 2023-04-27 01:36:47 -07:00
py-scikit-bio *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
py-valerius biology/py-valerius: New port: Python bioinformatics tools 2022-10-03 21:06:22 -07:00
py-xenaPython */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
pyfasta *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
python-nexus */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
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 Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio-executables Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
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 Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
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
sigviewer *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
sim4
slclust
smithwaterman
snpeff biology/snpeff: Update to 5.1 2022-12-19 12:50:00 -06:00
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 biology/star: Bump PORTREVISION for biology/htslib update 2023-01-05 19:27:16 -06:00
stringtie
subread
tabixpp biology/tabixpp: Deprecate 2023-01-22 11:01:57 -06:00
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 biology/tRNAscan-SE: Update to 2.0.11 2022-10-12 12:45:24 +01:00
ucsc-userapps
ugene
unikmer all: Bump PORTREVISION after lang/go{119,120} update 2023-04-08 10:13:25 -05:00
vcf2hap
vcf-split biology/vcf-split: Update to 0.1.5-4 2022-12-11 14:11:33 -06:00
vcflib biology/vcflib: Update to 1.0.7 2023-02-09 09:35:32 -06:00
vcftools
velvet
viennarna
vsearch biology/vsearch: Update to 2.22.1 2022-09-21 11:24:14 -05:00
vt biology/vt: Bump PORTREVISION for biology/htslib update 2023-01-05 19:19:19 -06:00
wfa2-lib */*: Sunset 12.3-RELEASE from ports tree 2023-03-30 18:59:51 -05:00
wise
Makefile biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics 2023-02-25 08:27:46 -06:00