Jason W. Bacon 2c0b2c08a0 biology/sra-tools: Update to 3.1.1 ... Numerous fixes and enhancements since 3.0.6 Changes: https://github.com/ncbi/sra-tools/commits/master/ All previous patches upstreamed Rewrote pkg-descr to be more introductory		2024-11-17 17:41:17 -06:00
..
abyss	biology/abyss: update 2.3.9 → 2.3.10	2024-11-04 12:36:54 -08:00
ad2vcf
andi
artemis
atac-seq
augustus
avida
babel
bamtools
bamutil
barrnap
bbmap
bcf-score
bcftools
bedtools
bfc
bifrost
bio-mocha
bioawk
biococoa
biolibc
biolibc-tools
bioparser
biosig
biosoup
biostar-tools	biology/biostar-tools: Update to 2.0	2024-11-07 18:44:28 -06:00
bolt-lmm
bowtie
bowtie2
btllib
bwa
canu
cd-hit
cdbfasta
checkm
chip-seq
clustal-omega
clustalw
coverm	lang/rust: Bump revisions after 1.82.0	2024-11-08 09:24:20 +01:00
cufflinks
cytoscape
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasda
fasta
fasta3
fastahack
fastani
fastdnaml
fastool
fastp	biology/fastp: Update to 0.24.0	2024-11-16 07:10:58 -06:00
fastq-trim
fastqc
fasttree
fastx-toolkit
fermi-lite
figtree
flash
fluctuate
freebayes
garlic
gatk
gcta
gemma
generand
gff2ps
gffread
gkl
gmap
gperiodic
graphlan
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy
igv
infernal
iolib
iqtree
jalview
jellyfish
kallisto
kmcp
lamarc
libbigwig
libcombine
libgff
libgtextutils
libneurosim
libnuml
libsbml
libsedml
linux-foldingathome
locarna
mafft
mapm3
mashmap
mca-calling
megahit
metaeuk
migrate
minimap2
mmseqs2
molden
mothur	biology/mothur: update 1.48.1 → 1.48.2	2024-11-04 23:25:49 -08:00
mrbayes
mummer
muscle
ncbi-blast+	Bump PORTREVISIONs after grpc shlib change in 2715f16944	2024-11-11 23:13:54 -04:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.9 → 28.0.10	2024-11-13 08:42:21 -08:00
ncbi-entrez-direct
ncbi-toolkit
ncbi-vdb	biology/ncbi-vdb: Deprecate and set expiration date to 2024-12-31	2024-11-06 20:39:54 +01:00
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
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
peak-classifier
pear-merger
phrap
phred
phyml
picard-tools
plink
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	biology/py-gtfparse: update 1.3.0 → 2.5.0	2024-11-16 02:27:19 -08:00
py-hits
py-htseq
py-libnuml
py-libsedml
py-loompy
py-macs2
py-macs3
py-mrcfile
py-multiqc	biology/py-multiqc: Update to 1.25.1	2024-11-15 19:28:59 -06:00
py-newick
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: update 3.5.2 → 3.6.3	2024-11-12 00:32:35 -08:00
py-pysam
py-PySCeS
py-python-libsbml	biology/py-python-libsbml: update 5.20.1 → 5.20.4	2024-11-12 02:18:13 -08:00
py-pywgsim
py-resdk	biology/py-resdk: update 21.2.0 → 21.2.1	2024-11-10 19:54:22 -08:00
py-scikit-bio
py-valerius
py-xenaPython
pyfasta
python-nexus
R-cran-Biobase
R-cran-BiocGenerics
R-cran-BiocManager
rainbow
rampler
readseq
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon
sam2pairwise
samtools
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqkit	biology/seqkit: update 2.8.2 → 2.9.0	2024-11-04 17:26:42 -08:00
seqtk
seqwish	biology/seqwish: Broken on 15 with clng-19	2024-11-16 02:27:18 -08:00
sigviewer
slclust
smithwaterman
snpeff
spoa
sra-tools	biology/sra-tools: Update to 3.1.1	2024-11-17 17:41:17 -06:00
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: update 0.17.0 → 0.18.0	2024-11-04 17:26:41 -08:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps	biology/ucsc-userapps: remove ONLY_FOR_ARCHS	2024-11-14 09:41:02 +01:00
ugene
unikmer
vcf2hap
vcf-split
vcflib
vcftools
velvet
viennarna
vsearch
vt
wfa2-lib
wise
Makefile