Eijiro Shibusawa 22df0dbcfa biology/gcta: chase the upgrade of OpenBLAS ... GCTA should modify the LAPACK functios calls, this is a temporary fix. See <https://github.com/jianyangqt/gcta/issues/59>. PR: 273219 Approved by: jwb@		2023-12-12 20:03:50 +01:00
..
abyss	*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2	2023-12-10 11:23:11 +01:00
ad2vcf
artemis
atac-seq	biology/atac-seq: Add curl to metaport deps	2023-07-28 09:35:04 -05:00
augustus	*/*: chase the upgrade of SuiteSparse	2023-10-15 11:03:17 +02:00
avida
babel	biology/babel: Update WWW	2023-10-30 23:37:03 +01:00
bamtools
bamutil
barrnap
bbmap
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 2.31.1	2023-11-08 10:42:09 -06:00
bfc
bifrost	biology/bifrost: Update to 1.3.1	2023-11-21 06:58:39 -06:00
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 0.2.6	2023-10-28 06:21:35 -05:00
biolibc-tools	biology/biolibc-tools: Update to 0.1.4.13	2023-10-29 17:41:02 -05:00
bioparser	biology/bioparser: update 3.0.15 → 3.1.0	2023-08-29 00:32:45 -07:00
biosig	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
biosoup	biology/biosoup: Install cmake files	2023-08-29 00:32:45 -07:00
biostar-tools	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
bolt-lmm	devel/boost*: bump all consumers after 1.83.0	2023-09-27 17:36:30 +03:00
bowtie	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
bowtie2	biology/bowtie2: Update to 2.5.2	2023-10-18 07:26:11 -05:00
btllib	biology/btllib: New port: Bioinformatics Technology Lab common code library	2023-07-21 15:24:04 -07:00
bwa
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	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
clustalw	biology/clustalw: Unbreak build for clang 16	2023-07-15 18:18:42 -05:00
cufflinks	devel/boost*: bump all consumers after 1.83.0	2023-09-27 17:36:30 +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 2.1.8	2023-07-08 00:45:48 -03:00
dsr-pdb	devel/boost*: bump all consumers after 1.83.0	2023-09-27 17:36:30 +03:00
edlib
emboss	biology/emboss: fix build on powerpc*	2023-12-03 12:13:43 +01:00
erminej
exonerate
fasda	biology/fasda: Update to 0.1.5	2023-10-28 06:32:20 -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	biology/fastq-trim: Update to 0.1.3	2023-10-28 06:34:21 -05:00
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
garlic
gatk	biology/gatk: Update 4.3.0.0 → 4.4.0.0	2023-06-04 15:02:58 -07:00
gcta	biology/gcta: chase the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
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	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
haplohseq	devel/boost*: bump all consumers after 1.83.0	2023-09-27 17:36:30 +03:00
hhsuite	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
hisat2
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: Update to 2.5.57	2023-11-14 20:09:46 -04:00
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	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-01 23:11:47 +01:00
iqtree	biology/iqtree: Update to 2.2.2.7	2023-09-04 23:45:37 -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
kallisto	biology/kallisto: Update to 0.50.1,1	2023-11-04 08:15:25 -05:00
kmcp	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
lamarc	biology/lamarc: Mark BROKEN on 14	2023-08-18 08:57:13 +02:00
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
libgtextutils
libneurosim	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
libnuml
libsbml	biology/libsbml: Update to 5.20.2	2023-09-30 08:44:19 +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: Fix tests	2023-07-17 09:22:42 -07:00
mafft
mapm3
mashmap	biology/mashmap: update 3.1.1 → 3.1.2	2023-12-06 00:34:56 -08:00
megahit
metaeuk	biology/metaeuk: Add NATIVE option	2023-07-14 17:31:14 -07:00
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	biology/mothur: Remove CC/CPP/CXX exports	2023-09-28 20:56:25 +02:00
mrbayes
mummer	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
muscle
ncbi-blast+	biology/ncbi-blast+: Update to 2.14.1	2023-08-26 07:57:04 -05:00
ncbi-cxx-toolkit	graphics/proj: Update to 9.2.1	2023-07-26 21:58:55 +02:00
ncbi-entrez-direct	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
ncbi-toolkit	*/*: Bump jpeg-turbo users treewide	2023-07-28 19:13:17 +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
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	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: Fix build	2023-08-05 22:05:05 +02:00
paml	biology/paml: Update to 4.10.7	2023-07-08 00:46:53 -03:00
pbbam
pbseqan
peak-classifier	biology/peak-classifier: Update to 0.1.4.13	2023-10-28 06:38:43 -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	biology/pooler: Update to 1.88	2023-09-10 08:06:18 -05:00
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	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
protomol	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-01 23:11:47 +01:00
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	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
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
py-dna-features-viewer	biology/py-dna-features-viewer: Update to 3.1.3	2023-11-04 17:11:34 -05:00
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	biology/py-Genesis-PyAPI: Add NO_ARCH	2023-08-01 00:42:07 +08:00
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-htseq	biology/py-htseq: Update to 2.0.4	2023-08-05 11:40:26 -05:00
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-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 1.15	2023-08-05 11:18:37 -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	biology/py-orange3-bioinformatics: Change RUN_DEPENDS from py-requests-cache to py-requests-cache0	2023-08-01 00:42:07 +08:00
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
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	biology/py-pyrodigal: update 3.1.0 → 3.1.1	2023-11-07 09:56:52 -08:00
py-pysam	biology/py-pysam: relax python version requirement	2023-12-03 14:51:05 +03:00
py-PySCeS	biology/py-PySCeS: Update 1.1.0 → 1.1.1	2023-07-25 23:20:25 -07:00
py-python-libsbml	biology/py-python-libsbml: relax python version requirement	2023-12-03 15:02:23 +03:00
py-pywgsim
py-resdk	biology/py-resdk: relax chardet limitation	2023-12-08 21:55:13 +01:00
py-scikit-bio	biology/py-scikit-bio: Update 0.5.8 → 0.5.9	2023-08-03 00:02:05 -07:00
py-valerius
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
rampler	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
readseq
recombine
rna-seq	biology/rna-seq: Add biology/star dep to metaport	2023-07-31 09:36:06 -05:00
ruby-bio
rubygem-bio	biology/rubygem-bio: Update to 2.0.5	2023-09-30 08:46:30 +08:00
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon	devel/onetbb: Update to 2021.11.0	2023-11-28 12:35:02 +01:00
sam2pairwise
samtools	biology/samtools: Update to 1.17	2023-02-24 17:27:21 -06:00
scrm
seaview	*/*: Bump jpeg-turbo users treewide	2023-07-28 19:13:17 +02:00
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
seqio
seqkit	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
seqtk	biology/seqtk: Update to 1.4	2023-05-23 17:42:13 -05:00
seqwish	biology/seqwish: Add comment	2023-11-05 15:07:52 -08:00
sigviewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
sim4
slclust
smithwaterman
snpeff	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
spoa	biology/spoa: update 4.0.7 → 4.1.0	2023-08-29 09:59:01 -07:00
sra-tools	biology/sra-tools: Update to 3.0.6	2023-08-10 12:17:24 -05:00
stacks
star	biology/star: Fix SIMD issue on non-amd64	2023-08-21 09:33:20 -05:00
stringtie
subread
tabixpp
taxonkit	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
treekin	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
treepuzzle
trimadap	biology/trimadap: drop GCC requirement on powerpc64le	2023-08-03 10:40:03 +00:00
trimmomatic
tRNAscan-SE
ucsc-userapps	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
ugene
unikmer	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
vcf2hap	biology/vcf2hap: Update to 0.1.6.7	2023-10-28 06:44:44 -05:00
vcf-split	biology/vcf-split: Update to 0.1.5.10	2023-10-28 06:41:39 -05:00
vcflib	biology/vcflib: not for armv6/7	2023-07-31 01:59:09 +03:00
vcftools	biology/vcftools: Unbreak build with clang 16	2023-07-15 20:29:00 -05:00
velvet
viennarna	biology/viennarna: update 2.6.3 → 2.6.4	2023-11-03 15:02:11 -07:00
vsearch	biology/vsearch: Update to 2.26.1	2023-11-26 06:32:55 -06:00
vt
wfa2-lib	biology/wfa2-lib: Update to 2.3.4	2023-09-29 13:24:07 -05:00
wise	*/*: Fix build with llvm16 on 13.2-STABLE	2023-07-26 02:48:20 +02:00
Makefile	biology/py-htseq: Python library for sequence analysis	2023-07-28 10:41:58 -05:00