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freebsd-ports/biology
History
Ashish SHUKLA aa8c0111bf
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
..
abyss
biology/abyss: update 2.3.7 → 2.3.8
2024-07-22 17:34:22 -07:00
ad2vcf
biology/ad2vcf: Update to 0.1.6.19
2024-05-19 08:41:41 -05:00
artemis
…
atac-seq
biology/atac-seq: Update to 0.2.0
2024-01-10 10:05:41 -06:00
augustus
*/*: chase SuiteSparse’s upgrade
2024-04-29 22:08:56 +02:00
avida
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
2023-12-31 01:37:05 +01:00
babel
biology/babel: Update WWW
2023-10-30 23:37:03 +01:00
bamtools
…
bamutil
…
barrnap
biology/barrnap: Update descr
2022-11-24 19:12:18 -08:00
bbmap
…
bcf-score
biology/bcf-score: Unbreak build with clang 16
2023-07-16 08:19:06 -05:00
bcftools
biology/bcftools: Move man pages to share/man
2024-03-02 18:38:43 +00:00
bedtools
biology/bedtools: Update to 2.31.1
2023-11-08 10:42:09 -06:00
bfc
…
bifrost
biology/bifrost: Update to 1.3.5
2024-03-18 09:29:43 -05:00
bio-mocha
biology/bio-mocha: Update to 1.16
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 0.2.6.4
2024-05-19 08:40:24 -05:00
biolibc-tools
biology/biolibc-tools: Move man pages to share/man
2024-03-02 18:44:44 +00:00
bioparser
biology/bioparser: update 3.0.15 → 3.1.0
2023-08-29 00:32:45 -07:00
biosig
biology/{.py-}biosig: update 2.6.0 → 2.6.1
2024-08-05 07:37:01 -07:00
biosoup
biology/biosoup: Install cmake files
2023-08-29 00:32:45 -07:00
biostar-tools
biology/biostar-tools: Update to 1.11
2024-06-03 06:38:30 -05:00
bolt-lmm
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
bowtie
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
bowtie2
biology/bowtie2: Update to 2.5.4
2024-05-24 06:33:53 -05:00
btllib
biology/btllib: update 1.7.2 → 1.7.3
2024-07-27 13:19:18 -07:00
bwa
MAN?PREFIX: eleminate its usage and move man to share/man
2024-01-10 09:16:01 +01:00
canu
biology/canu: Fix build with llvm16
2023-07-20 19:42:34 +02:00
cd-hit
biology/cd-hit: allow to build without GCC on libomp-less systems
2023-08-12 03:37:47 +02:00
cdbfasta
biology/cdbfasta: Update to 2023.07.10
2023-07-11 10:40:27 -05:00
checkm
biology/checkm: update 1.2.0 → 1.2.2
2024-04-23 01:40:35 -07:00
chip-seq
biology/chip-seq: Metaport for ChIP-Seq analysis
2023-06-14 16:23:37 -05:00
clustal-omega
…
clustalw
biology/clustalw: Unbreak build for clang 16
2023-07-15 18:18:42 -05:00
cufflinks
devel/boost: bump consumers after library update
2024-02-13 17:44:22 +03:00
cytoscape
biology/cytoscape: Broken on i386
2024-05-25 18:45:24 -07:00
ddocent
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
diamond
biology/diamond: Update to 2.1.9
2024-02-04 15:41:51 -04:00
dsr-pdb
devel/boost: bump consumers after library update
2024-02-13 17:44:22 +03:00
edlib
…
emboss
*/*: Refactor with IGNORE_WITH_MYSQL
2023-12-29 19:24:39 +01:00
erminej
…
exonerate
biology/exonerate: Moved man to share/man
2024-02-22 14:23:45 +01:00
fasda
biology/fasda: Move man pages to share/man
2024-03-02 19:03:05 +00:00
fasta
MAN[1-5]PREFIX: eleminate its usage and move man to share/man
2024-01-09 16:41:04 +01:00
fasta3
MAN?PREFIX: eleminate its usage and move man to share/man
2024-01-10 09:16:01 +01:00
fastahack
…
fastdnaml
…
fastool
…
fastp
biology/fastp: Update to 0.23.4
2023-05-31 10:40:00 -05:00
fastq-trim
biology/fastq-trim: Move man pages to share/man
2024-03-02 19:08:45 +00:00
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
fermi-lite
biology/fermi-lite: New port: Library anf tool for assembling Illumina short reads in small regions
2024-08-03 01:27:25 -07:00
figtree
…
flash
…
fluctuate
…
freebayes
biology/freebayes: Drop redundant tabixpp dep
2023-01-22 10:42:34 -06:00
garlic
…
gatk
biology/gatk: Update COMMENT
2024-08-04 13:13:15 -07:00
gcta
biology/gcta: Unbreak fetch
2024-07-08 17:04:44 -05:00
gemma
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
generand
biology/generand: Move man pages to share/man
2024-03-02 19:14:06 +00:00
gff2ps
biology/gff2ps: drop maintainership
2023-05-21 16:20:36 +00:00
gffread
…
gkl
biology/gkl: New port: Accelerated kernel library for genomics
2024-08-04 13:09:41 -07:00
gmap
…
gperiodic
accessibility/at-spi2-core: update to 2.46.0
2023-03-02 06:23:10 +01:00
graphlan
…
groopm
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
haplohseq
devel/boost: bump consumers after library update
2024-02-13 17:44:22 +03:00
hhsuite
*/*: bump PORTREVISION after OpenMPI upgrade
2024-02-18 10:29:31 +01:00
hisat2
…
hmmer
biology/hmmer: Moved man to share/man
2024-02-22 14:23:46 +01:00
htslib
biology/htslib: Moved man to share/man
2024-01-27 13:37:30 +01:00
hyphy
biology/hyphy: Update to 2.5.62
2024-06-21 13:58:09 -03:00
igv
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
infernal
biology/infernal: Moved man to share/man
2024-02-22 14:23:47 +01:00
iolib
biology/iolib: Moved man to share/man
2024-02-22 14:23:48 +01:00
iqtree
biology/iqtree: Update to 2.3.5
2024-07-01 18:28:31 -03:00
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: Move man pages to share/man
2024-03-02 19:17:36 +00:00
kallisto
biology/kallisto: Update to 0.51.0,1
2024-07-27 07:02:57 -05:00
kmcp
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
lamarc
biology/lamarc: Mark BROKEN on 14
2023-08-18 08:57:13 +02:00
libbigwig
biology/libbigwig: Fix name-clashing in roundup
2023-12-28 18:03:34 -05:00
libcombine
biology/libcombine: Fix build with libsbml 5.20.0
2023-05-27 12:24:05 +08:00
libgff
…
libgtextutils
…
libneurosim
devel/automake: Update to 1.17
2024-07-20 13:27:02 +02:00
libnuml
…
libsbml
biology/libsbml: Fix build with libxml2 2.12.0+
2024-06-18 12:05:09 +08:00
libsedml
biology/libsedml: Fix build with libsbml 5.20.0
2023-05-27 12:24:05 +08:00
linux-foldingathome
…
locarna
biology/locarna: Move man pages to share/man
2024-03-03 10:04:08 +00:00
mafft
biology/mafft: Moved man to share/man
2024-02-22 14:23:49 +01:00
mapm3
…
mashmap
biology/mashmap: Broken on armv7
2024-01-12 17:57:41 -08:00
megahit
biology/megahit: Add cmake patch to respect ports build flags
2022-11-24 08:10:13 -06:00
metaeuk
biology/metaeuk: update 6 → 7
2024-06-01 01:10:52 -07:00
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
…
molden
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
mothur
biology/mothur: update 1.48.0 → 1.48.1
2024-05-16 01:56:44 -07:00
mrbayes
…
mummer
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
muscle
…
ncbi-blast+
devel/grpc: Update to 1.62.0
2024-03-09 22:05:20 +08:00
ncbi-cxx-toolkit
biology/ncbi-cxx-toolkit: update 28.0.6 → 28.0.7
2024-08-07 10:06:19 -07:00
ncbi-entrez-direct
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
ncbi-toolkit
MANPREFIX: eliminate its usage
2024-01-12 16:11:29 +01:00
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: Attempt to fix build on i386
2024-04-28 00:10:02 -07:00
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
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8
2023-12-25 16:59:52 +08:00
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
biology/p5-BioPerl: Update to 1.007008
2023-10-11 20:57:41 +08:00
p5-BioPerl-Run
…
p5-transdecoder
p5-transdecoder: Update to 5.7.1
2023-08-05 15:58:40 -05:00
p5-TrimGalore
biology/p5-TrimGalore: Update to 0.6.10
2024-07-23 11:01:28 -04:00
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
peak-classifier
biology/peak-classifier: Clean up USES=python
2024-04-05 08:43:40 +08:00
pear-merger
MANPREFIX: eliminate its usage
2024-01-12 16:11:29 +01:00
phrap
…
phred
…
phyml
biology/phyml: fix build on non-amd64
2024-06-16 17:25:18 +02:00
picard-tools
*/*: Refactor java/openjdk7 removal
2023-04-04 13:10:53 -05:00
plink
*/*: bump PORTREVISION after the upgrade to OpenBLAS
2024-06-21 19:49:24 +02:00
pooler
biology/pooler: Moved man to share/man
2024-02-22 14:23:50 +01:00
primer3
biology/primer3: Fix build with llvm16
2023-08-05 20:55:50 +02:00
prodigal
biology/prodigal: Update 2.6.3-7 → 2.6.3-16
2023-07-22 00:37:33 -07:00
prodigy-lig
biology/prodigy-lig: update 1.1.0 → 1.1.1
2024-04-26 22:55:21 -07:00
protomol
graphics/tiff: Update to 4.6.0
2024-04-27 14:44:59 +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
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 to 1.83
2024-04-08 02:29:37 +00:00
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 0.10.0 → 0.11.0
2024-02-12 15:07:35 -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 4.9
2024-06-20 10:38:00 +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
biology/py-dna-features-viewer: Update to 3.1.3
2023-11-04 17:11:34 -05:00
py-dnaio
biology/py-dnaio: Update to 1.2.1
2024-07-04 09:15:39 +00:00
py-ete3
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-Genesis-PyAPI
biology/py-Genesis-PyAPI: Add NO_ARCH
2023-08-01 00:42:07 +08:00
py-gffutils
biology/py-gffutils: update 0.11.1 → 0.13
2024-06-16 18:20:35 -07:00
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-htseq
biology/py-htseq: Fix build with python-3.11
2024-01-21 07:13:35 +00:00
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
biology/py-macs2: Update to 2.2.9.1
2023-08-06 13:17:52 -05:00
py-macs3
all: drop support for FreeBSD 13.2 which reached EOL today
2024-07-01 22:27:23 +02:00
py-mrcfile
biology/py-mrcfile: update 1.5.2 → 1.5.3
2024-07-26 01:57:55 -07:00
py-multiqc
devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml
2024-07-07 16:05:33 +08:00
py-newick
biology/py-newick: Add new port
2024-02-03 00:58:29 +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
devel/py-setuptools-scm: update to 8.0.4
2024-02-29 02:18:32 -05:00
py-orange3-single-cell
biology/py-orange3-single-cell: Add NO_ARCH
2023-08-01 00:42:07 +08:00
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 0.3.22
2023-12-16 07:59:37 -06:00
py-pyfaidx
all: remove explicit versions in USES=python for "3.x+"
2023-06-27 21:34:34 +02:00
py-pyrodigal
biology/py-pyrodigal: update 3.5.0 → 3.5.1
2024-07-22 17:34:23 -07:00
py-pysam
biology/py-pysam: update 0.22.0 → 0.22.1
2024-04-25 07:52:08 -07:00
py-PySCeS
biology/py-PySCeS: update 1.2.1 → 1.2.2
2024-08-03 01:27:31 -07:00
py-python-libsbml
biology/py-python-libsbml: relax python version requirement
2023-12-03 15:02:23 +03:00
py-pywgsim
biology/py-pywgsim: fix build
2024-06-07 11:11:35 +03:00
py-resdk
biology/py-resdk: update 21.1.0 → 21.2.0
2024-07-12 01:58:00 -07:00
py-scikit-bio
biology/py-scikit-bio: update 0.6.1 → 0.6.2
2024-07-12 22:17:53 -07:00
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
biology/python-nexus: Update to 2.9.0 and fix build with python-3.11
2024-02-03 00:58:29 +00:00
R-cran-Biobase
biology/R-cran-Biobase: New port
2023-12-15 13:55:44 +01:00
R-cran-BiocGenerics
biology/R-cran-BiocGenerics: New port
2023-12-15 13:55:44 +01:00
R-cran-BiocManager
biology/R-cran-BiocManager: Update version 1.30.22=>1.30.23
2024-05-12 01:10:24 +02:00
rainbow
…
rampler
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
readseq
…
rna-seq
biology/rna-seq: Add biology/star dep to metaport
2023-07-31 09:36:06 -05:00
ruby-bio
Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby
2023-01-14 17:08:33 -06:00
rubygem-bio
biology/rubygem-bio: Update to 2.0.5
2023-09-30 08:46:30 +08:00
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
salmon
devel/onetbb: Update to 2021.13.0
2024-07-04 13:39:44 +02:00
sam2pairwise
…
samtools
biology/samtools: Move man pages to share/man
2024-03-02 19:40:58 +00:00
scrm
biology/scrm: Move man pages to share/man
2024-03-02 19:59:23 +00:00
seaview
MANPREFIX: eliminate its usage
2024-01-12 16:11:29 +01:00
seqan
…
seqan1
…
seqan3
biology/seqan3: update 3.2.0 → 3.3.0
2023-09-10 11:10:47 -07:00
seqan-apps
biology/seqan-apps: Fix build with llvm16
2023-08-06 23:53:04 +02:00
seqkit
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
seqtk
biology/seqtk: Update to 1.4
2023-05-23 17:42:13 -05:00
seqwish
biology/seqwish: update 0.7.9 → 0.7.10
2024-05-18 10:29:58 -07:00
sigviewer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
slclust
…
smithwaterman
…
snpeff
*/*: Update WWW to use HTTPS for sourceforge.net projects
2023-11-06 11:03:47 +01:00
spoa
biology/spoa: Broken on i386
2024-04-11 21:05:12 -07:00
sra-tools
cleanup: remove occurrences of WITH_DEBUG
2024-04-12 08:04:05 +02:00
stacks
biology/stacks: Unbreak build on aarch64
2024-05-28 16:17:25 -05:00
star
biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
2024-05-05 09:58:47 -05:00
stringtie
…
subread
…
tabixpp
biology/tabixpp: Deprecate
2023-01-22 11:01:57 -06:00
taxonkit
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
treekin
biology/treekin: Move man pages to share/man
2024-03-02 20:02:27 +00:00
treepuzzle
…
trimadap
biology/trimadap: drop GCC requirement on powerpc64le
2023-08-03 10:40:03 +00:00
trimmomatic
biology/trimmomatic: Release to ports@
2024-04-05 19:12:17 -05:00
tRNAscan-SE
biology/tRNAscan-SE: Update to 2.0.11
2022-10-12 12:45:24 +01:00
ucsc-userapps
biology/ucsc-userapps: Replace dependencies
2023-12-30 08:16:41 +01:00
ugene
MAN?PREFIX: eleminate its usage and move man to share/man
2024-01-10 09:16:01 +01:00
unikmer
all: Bump after lang/go121 update
2024-08-09 06:24:08 +00:00
vcf2hap
biology/vcf2hap: Move man pages to share/man
2024-03-02 20:07:47 +00:00
vcf-split
biology/vcf-split: Move man pages to share/man
2024-03-02 20:04:57 +00:00
vcflib
biology/vcflib: add upstream reference for zig >= 0.11
2024-05-20 16:42:43 +02:00
vcftools
biology/vcftools: Move man pages to share/man
2024-03-02 20:35:56 +00:00
velvet
…
viennarna
biology/viennarna: Move man pages to share/man
2024-03-02 20:35:56 +00:00
vsearch
biology/vsearch: Update to 2.28.1
2024-05-01 08:41:05 -05:00
vt
biology/vt: Bump PORTREVISION for biology/htslib update
2023-01-05 19:19:19 -06:00
wfa2-lib
biology/wfa2-lib: fix build without libomp
2024-08-04 14:00:47 +02:00
wise
*/*: Fix build with llvm16 on 13.2-STABLE
2023-07-26 02:48:20 +02:00
Makefile
biology/gkl: New port: Accelerated kernel library for genomics
2024-08-04 13:09:41 -07:00