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freebsd-ports/biology
History
Charlie Li 9a80a6ee5e
devel/py-setuptools: convert individual consumers to ${PY_SETUPTOOLS} 
Currently a no-op, but in the future outputs the correct setuptools
port depending on whether USES_PYTHON=distutils is specified.

With hat: python
PR: 270510, 270358
2023-07-17 20:53:09 -04:00
..
abyss
biology/abyss: Fix build with llvm15
2023-06-07 09:25:09 +02:00
ad2vcf
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
artemis
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
atac-seq
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
augustus
*/*: bump PORTREVISION after the upgrade of SuiteSparse
2023-07-01 18:11:11 +02:00
avida
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
babel
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
bamtools
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
bamutil
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
barrnap
biology/barrnap: Update descr
2022-11-24 19:12:18 -08:00
bbmap
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
bcf-score
biology/bcf-score: Unbreak build with clang 16
2023-07-16 08:19:06 -05:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
bifrost
biology/bifrost: Portability fixes
2023-07-16 08:40:30 -05:00
bio-mocha
biology/bio-mocha: Update to 1.16
2023-01-05 17:21:03 -06:00
bioawk
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
biosig
*/*: bump PORTREVISION after the upgrade of SuiteSparse
2023-07-01 18:11:11 +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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
bowtie2
biology/bowtie2: Update to 2.5.1
2023-01-21 16:30:48 -06:00
bwa
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
canu
*/*: Refactor java/openjdk7 removal
2023-04-04 13:10:53 -05:00
cd-hit
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
cdbfasta
biology/cdbfasta: Update to 2023.07.10
2023-07-11 10:40:27 -05:00
checkm
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
chip-seq
biology/chip-seq: Metaport for ChIP-Seq analysis
2023-06-14 16:23:37 -05:00
clustal-omega
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
clustalw
biology/clustalw: Unbreak build for clang 16
2023-07-15 18:18:42 -05:00
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 2.1.8
2023-07-08 00:45:48 -03:00
dsr-pdb
*/*: bump all direct Boost cunsumers
2023-04-27 21:25:55 +03:00
edlib
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
emboss
biology/emboss: Ignore with mysql 8.0
2023-02-01 04:39:38 -06:00
erminej
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
exonerate
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fasda
biology/fasda: Update to 0.1.3
2023-06-10 06:57:56 -05:00
fasta
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fasta3
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fastahack
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fastdnaml
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fastool
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fastp
biology/fastp: Update to 0.23.4
2023-05-31 10:40:00 -05:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fastx-toolkit
biology/fastx-toolkit: Unbreak build on 14-CURRENT
2023-03-07 11:28:13 -06:00
figtree
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
flash
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
fluctuate
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
freebayes
biology/freebayes: Drop redundant tabixpp dep
2023-01-22 10:42:34 -06:00
garlic
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
gff2ps
biology/gff2ps: drop maintainership
2023-05-21 16:20:36 +00:00
gffread
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
gmap
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
gperiodic
accessibility/at-spi2-core: update to 2.46.0
2023-03-02 06:23:10 +01:00
graphlan
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
groopm
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
haplohseq
biology/haplohseq: Fix build on FreeBSD 14
2023-07-09 11:37:39 -05:00
hhsuite
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
hisat2
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
hmmer
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
htslib
biology/htslib: fix build on armv7
2023-04-18 23:55:29 +02:00
hyphy
biology/hyphy: fix build on armv7
2023-06-30 14:00:28 +02:00
igv
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
infernal
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
iolib
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
iqtree
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
jalview
biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1
2023-06-18 02:58:53 -07:00
jellyfish
biology/jellyfish: Bump PORTREVISION for biology/htslib update
2023-01-05 19:24:44 -06:00
kallisto
biology/kallisto: Tag only for 64-bit architectures
2023-07-14 11:12:06 -05:00
kmcp
biology/kmcp: Update 0.9.2 → 0.9.3
2023-07-17 00:09:00 -07:00
lamarc
biology/lamarc: Refactor after wxgtk28 removal
2022-12-31 04:54:58 +01:00
libbigwig
biology/libbigwig: Update 0.4.6 → 0.4.7
2023-07-17 00:09:00 -07:00
libcombine
biology/libcombine: Fix build with libsbml 5.20.0
2023-05-27 12:24:05 +08:00
libgff
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
libgtextutils
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
libneurosim
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
libnuml
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
libsbml
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
libsedml
biology/libsedml: Fix build with libsbml 5.20.0
2023-05-27 12:24:05 +08:00
linux-foldingathome
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
locarna
biology/locarna: Fix tests
2023-07-17 09:22:42 -07:00
mafft
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
mapm3
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
mashmap
biology/mashmap: New port: Fast approximate aligner for long DNA sequences
2023-07-10 18:44:34 -07:00
megahit
biology/megahit: Add cmake patch to respect ports build flags
2022-11-24 08:10:13 -06:00
metaeuk
biology/metaeuk: Add NATIVE option
2023-07-14 17:31:14 -07:00
migrate
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
minimap2
biology/minimap2: Update to 2.25
2023-04-29 09:53:40 -05:00
mmseqs2
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
molden
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
mothur
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
mrbayes
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
mummer
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
muscle
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
ncbi-blast+
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
ncbi-cxx-toolkit
biology/ncbi-cxx-toolkit: Update 26.0.1 → 27.0.0
2023-06-26 21:41:39 -07:00
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
biology/ngs-sdk: Update 2.11.2 → 3.0.1
2023-06-26 15:51:40 -07:00
p5-AcePerl
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-ASN1-EntrezGene
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Cluster
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Coordinate
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Das
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Das-Lite
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-DB-EMBL
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-DB-NCBIHelper
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-FeatureIO
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-GFF3
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Glite
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Graphics
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-MAGETAB
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-NEXUS
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Phylo
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-SCF
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-Bio-Variation
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-BioPerl
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-BioPerl-Run
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
p5-transdecoder
biology/p5-transdecoder: Update to 5.7.0
2023-01-30 16:30:54 -06:00
p5-TrimGalore
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
paml
biology/paml: Update to 4.10.7
2023-07-08 00:46:53 -03:00
pbbam
biology/pbbam: Bump PORTREVISION for biology/htslib update
2023-01-05 19:25:09 -06:00
pbseqan
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
peak-classifier
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
pear-merger
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
phrap
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
phred
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
biology/pooler: update to 1.86
2022-12-19 08:56:15 +01:00
primer3
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
prodigal
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
prodigy-lig
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
protomol
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-biopython
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-biosig
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-bx-python
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-crossmap
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-cutadapt
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-deeptools
biology/py-deeptools: Update to 3.5.2
2023-06-19 07:09:17 -05:00
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
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-ete3
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-Genesis-PyAPI
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-gffutils
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-goatools
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-gtfparse
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-hits
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
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
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-macs2
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-mrcfile
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-multiqc
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
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
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-orange3-single-cell
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-pandas-charm
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
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
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-pyrodigal
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-pysam
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-PySCeS
biology/py-PySCeS: Update 1.0.3 → 1.1.0
2023-06-26 08:53:04 -07:00
py-python-libsbml
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-pywgsim
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
2023-01-11 18:58:34 +03:00
py-resdk
devel/py-setuptools: convert individual consumers to ${PY_SETUPTOOLS}
2023-07-17 20:53:09 -04:00
py-scikit-bio
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-valerius
biology/py-valerius: New port: Python bioinformatics tools
2022-10-03 21:06:22 -07:00
py-xenaPython
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
pyfasta
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
python-nexus
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
rainbow
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
rampler
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
readseq
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
recombine
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
samtools
biology/samtools: Update to 1.17
2023-02-24 17:27:21 -06:00
scrm
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seaview
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seqan
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seqan1
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seqan3
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
seqan-apps
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seqio
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
seqkit
biology/seqkit: Update 2.4.0 → 2.5.0
2023-07-16 21:37:53 -07:00
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
Remove WWW lines that have been moved into Makefiles
2022-09-08 17:46:38 +02:00
slclust
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
smithwaterman
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
snpeff
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
star
biology/star: Bump PORTREVISION for biology/htslib update
2023-01-05 19:27:16 -06:00
stringtie
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
subread
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
trimadap
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
trimmomatic
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
tRNAscan-SE
biology/tRNAscan-SE: Update to 2.0.11
2022-10-12 12:45:24 +01:00
ucsc-userapps
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
ugene
Mk/Uses: always use colon for build/run suffix
2022-09-11 12:20:14 +02:00
unikmer
all: Bump PORTREVISION after lang/go{119,120} update
2023-04-08 10:13:25 -05:00
vcf2hap
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
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
biology/vcftools: Unbreak build with clang 16
2023-07-15 20:29:00 -05:00
velvet
Remove WWW entries moved into port Makefiles
2022-09-07 23:58:51 +02:00
viennarna
biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr
2023-07-16 14:38:39 -07:00
vsearch
biology/vsearch: Update to 2.23.0
2023-07-08 14:10:45 -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
*/*: llvm15 build fixes
2023-05-17 18:30:15 +02:00
Makefile
biology/locarna: New port: LocARNA provides several tools for the structural analysis of RNA
2023-07-16 14:54:52 -07:00