Jason W. Bacon 93db8fd309 biology/biolibc: Update to 0.2.6.4 ... bl_sam_copy(): Make sure all fields are properly initialized		2024-05-19 08:40:24 -05:00
..
abyss
ad2vcf
artemis
atac-seq
augustus	*/*: chase SuiteSparse’s upgrade	2024-04-29 22:08:56 +02:00
avida
babel
bamtools
bamutil
barrnap
bbmap
bcf-score
bcftools
bedtools
bfc
bifrost
bio-mocha
bioawk
biococoa
biolibc	biology/biolibc: Update to 0.2.6.4	2024-05-19 08:40:24 -05:00
biolibc-tools
bioparser
biosig	*/*: chase SuiteSparse’s upgrade	2024-04-29 22:08:56 +02:00
biosoup
biostar-tools
bolt-lmm
bowtie
bowtie2
btllib	biology/btllib: update 1.7.1 → 1.7.2	2024-04-09 00:40:58 -07:00
bwa
canu
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
cufflinks
cytoscape
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasda
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastq-trim
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes
garlic
gatk
gcta
gemma
generand
gff2ps
gffread
gmap
gperiodic
graphlan
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to 2.5.61	2024-05-16 13:08:06 -03:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to 2.3.4	2024-05-16 13:08:07 -03:00
jalview
jellyfish
kallisto	biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir	2024-05-05 09:47:05 -05:00
kmcp	all: Bump after lang/go121 update	2024-05-13 17:56:04 +00:00
lamarc
libbigwig
libcombine
libgff
libgtextutils
libneurosim
libnuml
libsbml
libsedml
linux-foldingathome
locarna
mafft
mapm3
mashmap
megahit
metaeuk
migrate	biology/migrate: Use system zlib instead of excluding it from extract	2024-04-12 21:07:33 +01:00
minimap2	biology/minimap2: Fix man prefix	2024-04-17 17:52:15 -05:00
mmseqs2
molden
mothur	biology/mothur: update 1.48.0 → 1.48.1	2024-05-16 01:56:44 -07:00
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.3 → 28.0.4	2024-05-07 01:26:36 -07:00
ncbi-entrez-direct	all: Bump after lang/go121 update	2024-05-13 17:56:04 +00:00
ncbi-toolkit
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
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	biology/p5-TrimGalore: Release to ports@	2024-04-05 19:12:17 -05:00
paml
pbbam
peak-classifier	biology/peak-classifier: Clean up USES=python	2024-04-05 08:43:40 +08:00
pear-merger
phrap
phred
phyml
picard-tools
plink
pooler
primer3
prodigal
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
py-bcbio-gff
py-biom-format
py-biopython	biology/py-biopython: Update to 1.83	2024-04-08 02:29:37 +00:00
py-biosig	biology/{,py-}biosig: update 2.5.2 → 2.6.0	2024-04-05 18:04:45 -07:00
py-bx-python
py-crossmap
py-cutadapt	biology/py-cutadapt: Release to ports@	2024-04-05 19:12:16 -05:00
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio	biology/py-dnaio: Release to ports@	2024-04-10 18:41:31 -05:00
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: Mark not for i386	2024-04-18 18:02:57 -05:00
py-mrcfile
py-multiqc
py-newick
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal
py-pysam	biology/py-pysam: update 0.22.0 → 0.22.1	2024-04-25 07:52:08 -07:00
py-PySCeS
py-python-libsbml
py-pywgsim
py-resdk	biology/py-resdk: update 20.0.0 → 21.1.0	2024-04-05 18:04:45 -07:00
py-scikit-bio	biology/py-scikit-bio: update 0.5.9 → 0.6.0	2024-04-05 18:04:46 -07:00
py-valerius
py-xenaPython
pyfasta
python-nexus
R-cran-Biobase
R-cran-BiocGenerics
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
readseq
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon	devel/onetbb: Update to 2021.12.0	2024-04-17 13:28:34 +02:00
sam2pairwise
samtools
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqkit	biology/seqkit: update 2.8.1 → 2.8.2	2024-05-18 09:52:19 -07:00
seqtk
seqwish	biology/seqwish: update 0.7.9 → 0.7.10	2024-05-18 10:29:58 -07:00
sigviewer
slclust
smithwaterman
snpeff
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
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	2024-05-13 17:56:04 +00:00
treekin
treepuzzle
trimadap
trimmomatic	biology/trimmomatic: Release to ports@	2024-04-05 19:12:17 -05:00
tRNAscan-SE
ucsc-userapps
ugene
unikmer	all: Bump after lang/go121 update	2024-05-13 17:56:04 +00:00
vcf2hap
vcf-split
vcflib	biology/vcflib: Update to 1.0.10	2024-04-22 07:42:04 -05:00
vcftools
velvet
viennarna
vsearch	biology/vsearch: Update to 2.28.1	2024-05-01 08:41:05 -05:00
vt
wfa2-lib	biology/wfa2-lib: Update to 2.3.5	2024-04-22 07:42:04 -05:00
wise
Makefile	biology/pbseqan: Remove expired port	2024-05-05 13:35:44 +02:00