Nuno Teixeira dc29da5db6 biology/migrate: Fix extract ... Extract fails on aarch64 with error: (sample) "dynsections.js: Cannot restore extended attributes: com.apple.quarantine com.apple.quarantine: No such file or directory" tar: Error exit delayed from previous errors.- Fix extract with: --no-same-owner --no-same-permissions		2024-03-27 12:36:40 +00:00
..
abyss	biology/abyss: Move man pages to share/man	2024-03-03 10:04:08 +00:00
ad2vcf	biology/ad2vcf: Move man pages to share/man	2024-03-02 18:32:34 +00:00
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 to SuiteSparse	2024-01-28 13:02:23 +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	biology/bcftools: Move man pages to share/man	2024-03-02 18:38:43 +00:00
bedtools
bfc
bifrost	biology/bifrost: Update to 1.3.5	2024-03-18 09:29:43 -05:00
bio-mocha
bioawk
biococoa
biolibc	biology/biolibc: Impelled to share/man	2024-01-23 15:51:25 +01:00
biolibc-tools	biology/biolibc-tools: Move man pages to share/man	2024-03-02 18:44:44 +00:00
bioparser
biosig	biology/biosig: Move man pages to share/man	2024-03-02 18:49:11 +00:00
biosoup
biostar-tools	biology/biostar-tools: Update to 1.10.1_3	2024-02-16 07:42:11 -06:00
bolt-lmm	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
bowtie
bowtie2	biology/bowtie2: Update to 2.5.3	2024-01-18 17:20:08 -06:00
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	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
cytoscape
ddocent
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
fastq-trim	biology/fastq-trim: Move man pages to share/man	2024-03-02 19:08:45 +00:00
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes
garlic
gatk	*/*: Replace format=bsdtar with format=ustar in tar archive operations	2024-02-18 17:48:08 -08:00
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	biology/generand: Move man pages to share/man	2024-03-02 19:14:06 +00:00
gff2ps
gffread
gmap
gperiodic
graphlan
groopm
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 2.5.58	2023-12-23 13:28:25 -04:00
igv
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
jalview
jellyfish	biology/jellyfish: Move man pages to share/man	2024-03-02 19:17:36 +00:00
kallisto
kmcp	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
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: 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
metaeuk	biology/metaeuk: Broken on powerpc64le	2024-02-04 10:27:53 -08:00
migrate	biology/migrate: Fix extract	2024-03-27 12:36:40 +00:00
minimap2	biology/minimap2: Move man page to share/man	2024-03-22 16:29:47 +09:00
mmseqs2
molden
mothur
mrbayes
mummer
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 28.0.0 → 28.0.2	2024-03-08 02:25:49 -08:00
ncbi-entrez-direct	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
ncbi-toolkit	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
ncbi-vdb
ngs-sdk	biology/ngs-sdk: Not for powerpc, powerpc64le	2024-02-02 13:33:37 -08:00
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
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbseqan
peak-classifier	biology/peak-classifier: Move man pages to share/man	2024-03-02 19:37:42 +00:00
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	biology/pooler: Moved man to share/man	2024-02-22 14:23:50 +01:00
primer3
prodigal
prodigy-lig	biology/prodigy-lig: update 1.0.1 → 1.1.0	2024-03-21 03:08:33 -07:00
protomol
psi88
py-bcbio-gff
py-biom-format
py-biopython
py-biosig
py-bx-python	biology/py-bx-python: update 0.10.0 → 0.11.0	2024-02-12 15:07:35 -08:00
py-crossmap
py-cutadapt	py-cutadapt: Update to 4.7	2024-03-16 08:31:06 -05:00
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio	devel/py-setuptools-scm: update to 8.0.4	2024-02-29 02:18:32 -05:00
py-ete3
py-Genesis-PyAPI
py-gffutils
py-goatools
py-gtfparse
py-hits
py-htseq	biology/py-htseq: Fix build with python-3.11	2024-01-21 07:13:35 +00:00
py-libnuml
py-libsedml
py-loompy
py-macs2
py-macs3	biology/py-macs3: Update to 3.0.1	2024-02-28 07:29:15 -06:00
py-mrcfile	biology/py-mrcfile: update 1.4.3 → 1.5.0	2024-01-19 23:47:54 -08:00
py-multiqc
py-newick	biology/py-newick: Add new port	2024-02-03 00:58:29 +00:00
py-ont-fast5-api
py-orange3-bioinformatics	devel/py-setuptools-scm: update to 8.0.4	2024-02-29 02:18:32 -05:00
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 3.2.2 → 3.3.0	2024-03-08 14:34:40 -08:00
py-pysam
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	devel/py-setuptools-scm: update to 8.0.4	2024-02-29 02:18:32 -05:00
py-scikit-bio
py-valerius
py-xenaPython
pyfasta
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: New port	2023-12-15 13:55:43 +01:00
rainbow
rampler
readseq
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon
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
seqan-apps
seqkit	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
seqtk
seqwish
sigviewer
slclust
smithwaterman
snpeff
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
treekin	biology/treekin: Move man pages to share/man	2024-03-02 20:02:27 +00:00
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	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
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: Move man pages to share/man	2024-03-02 20:35:56 +00:00
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: Move man pages to share/man	2024-03-02 20:35:56 +00:00
vt
wfa2-lib
wise
Makefile	biology/py-newick: Add new port	2024-02-03 00:58:29 +00:00