Piotr Kubaj 02b24eeb01 biology/metaeuk: fix build on powerpc64le by disabling openmp until libomp is fixed		2024-01-16 15:35:21 +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: Update to 0.2.0	2024-01-10 10:05:41 -06:00
augustus	*/*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0	2024-01-13 11:19:22 +01:00
avida	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
babel
bamtools
bamutil
barrnap
bbmap
bcf-score
bcftools
bedtools
bfc
bifrost	biology/bifrost: Update to 1.3.1	2023-11-21 06:58:39 -06:00
bio-mocha
bioawk
biococoa
biolibc
biolibc-tools
bioparser
biosig	*/*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0	2024-01-13 11:19:22 +01:00
biosoup
biostar-tools
bolt-lmm	*/*: bump PORTREVISION after the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
bowtie
bowtie2
btllib	biology/btllib: Temporarily not for non-64-bit architectures	2024-01-11 19:01:51 -08:00
bwa	MAN?PREFIX: eleminate its usage and move man to share/man	2024-01-10 09:16:01 +01:00
canu
cd-hit
cdbfasta
checkm
chip-seq
clustal-omega
clustalw
cufflinks
cytoscape
ddocent
diamond	biology/diamond: Fix build on main after import of clang 17	2023-12-29 14:57:14 -04:00
dsr-pdb
edlib
emboss	*/*: Refactor with IGNORE_WITH_MYSQL	2023-12-29 19:24:39 +01:00
erminej
exonerate
fasda
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
fastq-trim
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes
garlic
gatk	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
gcta	biology/gcta: chase the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
gemma	*/*: bump PORTREVISION after the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
generand
gff2ps
gffread
gmap
gperiodic
graphlan
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to 2.5.58	2023-12-23 13:28:25 -04:00
igv
infernal
iolib
iqtree
jalview
jellyfish
kallisto
kmcp	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
lamarc
libbigwig	biology/libbigwig: Fix name-clashing in roundup	2023-12-28 18:03:34 -05:00
libcombine
libgff
libgtextutils
libneurosim
libnuml
libsbml
libsedml
linux-foldingathome
locarna	biology/locarna: Fix build on 14.x and main	2023-12-13 23:11:55 -08:00
mafft	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
mapm3
mashmap	biology/mashmap: Broken on armv7	2024-01-12 17:57:41 -08:00
megahit
metaeuk	biology/metaeuk: fix build on powerpc64le by disabling openmp until libomp is fixed	2024-01-16 15:35:21 +01:00
migrate	MAN[1-5]PREFIX: eleminate its usage and move man to share/man	2024-01-09 16:41:04 +01:00
minimap2
mmseqs2
molden
mothur
mrbayes
mummer
muscle
ncbi-blast+	devel/grpc: Update to 1.60.0	2023-12-15 01:03:10 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 27.0.0 → 28.0.0	2024-01-05 01:38:14 -08:00
ncbi-entrez-direct	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
ncbi-toolkit	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
ncbi-vdb
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	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
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbseqan
peak-classifier
pear-merger	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
phrap
phred
phyml
picard-tools
plink	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
pooler
primer3
prodigal
prodigy-lig
protomol
psi88
py-bcbio-gff
py-biom-format
py-biopython
py-biosig
py-bx-python
py-crossmap
py-cutadapt
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio
py-ete3
py-Genesis-PyAPI
py-gffutils
py-goatools
py-gtfparse
py-hits
py-htseq
py-libnuml
py-libsedml
py-loompy
py-macs2
py-macs3	biology/py-macs3: Peak caller for TF binding sites	2024-01-10 09:19:56 -06:00
py-mrcfile
py-multiqc
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig	biology/py-pybigwig: Update to 0.3.22	2023-12-16 07:59:37 -06:00
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: update 3.1.1 → 3.2.1	2023-12-19 23:02:18 -08:00
py-pysam	biology/py-pysam: relax python version requirement	2023-12-03 14:51:05 +03:00
py-PySCeS	biology/py-PySCeS: Fix build by adding USES=localbase:ldflags	2023-12-14 00:43:06 -08:00
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
py-valerius
py-xenaPython
pyfasta
python-nexus
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: New port	2023-12-15 13:55:43 +01:00
rainbow
rampler
readseq
recombine	biology/recombine: Mark DEPRECATED	2023-12-17 14:11:36 +01:00
rna-seq
ruby-bio
rubygem-bio
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
scrm
seaview	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
seqan
seqan1
seqan3
seqan-apps
seqio	biology/seqio: Mark DEPRECATED	2023-12-17 14:11:36 +01:00
seqkit	all: Bump PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
seqtk
seqwish
sigviewer
sim4	biology/sim4: fix EXPIRATION_DATE	2023-12-18 09:29:31 +01:00
slclust
smithwaterman
snpeff
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: update 0.15.0 → 0.15.1	2023-12-19 23:02:18 -08:00
treekin	*/*: chase the upgrade of BLAS / LAPACK to 3.12.0	2024-01-01 12:49:51 +01:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
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 PORTREVISION after lang/go* update	2023-12-07 02:22:10 +00:00
vcf2hap
vcf-split
vcflib	lang/zig: update to 0.11.0	2024-01-01 06:37:19 +01:00
vcftools
velvet
viennarna	*/*: chase the upgrade of BLAS / LAPACK to 3.12.0	2024-01-01 12:49:51 +01:00
vsearch	biology/vsearch: Update to 2.26.1	2023-11-26 06:32:55 -06:00
vt
wfa2-lib
wise
Makefile	biology/py-macs3: Peak caller for TF binding sites	2024-01-10 09:19:56 -06:00