Jason W. Bacon 0ece2dbac7 biology/trimadap: Update to 0.1.4 ... Update to latest commit, with new MIT license Add support for other architectures using SIMDE Reported by: fuz Reviewed by: fuz Differential Revision: https://reviews.freebsd.org/D47129		2024-10-18 06:37:12 -05:00
..
abyss	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
ad2vcf	biology/ad2vcf: Update to 0.1.6.19	2024-05-19 08:41:41 -05:00
andi	biology/andi: New ports: Efficient estimation of evolutionary distances	2024-09-07 14:31:10 -07:00
artemis
atac-seq	biology/atac-seq: Update to 0.2.0	2024-01-10 10:05:41 -06:00
augustus	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
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	*/*: Bump dependencioes after devel/jsoncpp update	2024-09-12 09:20:06 -07:00
bamutil
barrnap
bbmap
bcf-score	biology/bcf-score: Update to 1.20	2024-10-09 17:23:09 -05:00
bcftools	biology/bcftools: Update to 1.21	2024-10-09 17:23:09 -05:00
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 1.20	2024-10-09 17:23:10 -05:00
bioawk
biococoa
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
biosig	biology/biosig: fix build with libc++ 19	2024-10-11 19:30:49 +02:00
biosoup
biostar-tools	biology/biostar-tools: Update to 1.11	2024-06-03 06:38:30 -05:00
bolt-lmm	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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 2.5.4	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	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
cd-hit
cdbfasta
checkm	biology/checkm: update 1.2.0 → 1.2.2	2024-04-23 01:40:35 -07:00
chip-seq
clustal-omega
clustalw
coverm	biology/coverm: Broken on i386	2024-10-06 11:31:38 -07:00
cufflinks	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
cytoscape	biology/cytoscape: Broken on i386	2024-05-25 18:45:24 -07:00
ddocent
diamond	biology/diamond: Update to 2.1.9	2024-02-04 15:41:51 -04:00
dsr-pdb	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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
fastani	biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation	2024-09-20 20:03:29 -07:00
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
fermi-lite	biology/fermi-lite: Add ONLY_FOR_ARCHS line	2024-09-19 14:05:26 -07:00
figtree
flash
fluctuate
freebayes
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
gffread
gkl	biology/gkl: New port: Accelerated kernel library for genomics	2024-08-04 13:09:41 -07:00
gmap
gperiodic
graphlan
groopm
haplohseq	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +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: Update to 1.21	2024-10-09 17:23:08 -05:00
hyphy	biology/hyphy: Update to 2.5.62	2024-06-21 13:58:09 -03:00
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	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
jalview
jellyfish	biology/jellyfish: Move man pages to share/man	2024-03-02 19:17:36 +00:00
kallisto	biology/kallisto: Update to 0.51.1,1	2024-09-19 17:46:47 -05:00
kmcp	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
lamarc
libbigwig	biology/libbigwig: Fix name-clashing in roundup	2023-12-28 18:03:34 -05:00
libcombine
libgff
libgtextutils
libneurosim	devel/automake: Update to 1.17	2024-07-20 13:27:02 +02:00
libnuml
libsbml	biology/libsbml: Update to 5.20.4	2024-09-09 02:36:57 +08:00
libsedml
linux-foldingathome	biology/linux-foldingathome: Point MASTER_SITES to the new location	2024-08-12 14:58:05 +02:00
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: 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
mothur	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +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+: Fix build with grpc 1.67.0+	2024-10-14 13:26:28 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.8 → 28.0.9	2024-10-06 11:08:26 -07:00
ncbi-entrez-direct	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
ncbi-toolkit	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
ncbi-vdb
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-TrimGalore	biology/p5-TrimGalore: Update to 0.6.10	2024-07-23 11:01:28 -04:00
paml
pbbam	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
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
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
prodigal
prodigy-lig	biology/prodigy-lig: update 1.1.2 → 1.1.3	2024-10-15 08:33:52 -07:00
protomol	graphics/tiff: Update to 4.6.0	2024-04-27 14:44:59 +02:00
psi88
py-bcbio-gff
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
py-cutadapt	biology/py-cutadapt: update to 4.9	2024-06-20 10:38:00 +02:00
py-deeptools
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	biology/py-dnaio: Update to 1.2.1	2024-07-04 09:15:39 +00:00
py-ete3
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: update 0.11.1 → 0.13	2024-06-16 18:20:35 -07:00
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 3.0.2	2024-09-14 08:23:32 -05:00
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
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 3.5.1 → 3.5.2	2024-09-05 01:48:51 -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
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: Update version 1.30.24=>1.30.25	2024-09-08 19:28:55 +02:00
rainbow
rampler
readseq
rna-seq
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	*/*: bump consumers after devel/boost* update	2024-10-03 13:25:14 +03:00
sam2pairwise
samtools	biology/samtools: Update to 1.21	2024-10-09 17:23:09 -05:00
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
seqan-apps
seqan1
seqan3
seqkit	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
seqtk
seqwish	biology/seqwish: update 0.7.9 → 0.7.10	2024-05-18 10:29:58 -07:00
sigviewer
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
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: Update to 0.1.4	2024-10-18 06:37:12 -05:00
trimmomatic	biology/trimmomatic: Release to ports@	2024-04-05 19:12:17 -05:00
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 after lang/go121 update	2024-08-09 06:24:08 +00:00
vcf-split	biology/vcf-split: Move man pages to share/man	2024-03-02 20:04:57 +00:00
vcf2hap	biology/vcf2hap: Move man pages to share/man	2024-03-02 20:07:47 +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
wfa2-lib	biology/wfa2-lib: fix build without libomp	2024-08-04 14:00:47 +02:00
wise	all: drop support for expired FreeBSD 14.0	2024-10-01 20:56:20 +02:00
Makefile	biology/coverm: New port: Read coverage calculator for metagenomics	2024-10-04 20:09:27 -07:00