Yuri Victorovich e41256b1f3 biology/libcombine: Update 0.2.19 -> 0.2.20 ... Reported by: portscout		2022-12-08 03:11:24 -08:00
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abyss
ad2vcf
artemis
augustus	biology/augustus: New port: Genome annotation tool	2022-11-25 15:55:09 -08:00
avida
babel
bamtools
bamutil
barrnap	biology/barrnap: Update descr	2022-11-24 19:12:18 -08:00
bbmap
bcftools
bedtools
bfc
bio-mocha
bioawk
biococoa
biolibc
biolibc-tools
bioparser
biosig	*/*: bump PORTREVISION after the upgrade of math/suitesparse*	2022-11-27 12:09:57 +01:00
biosoup
biostar-tools
bolt-lmm
bowtie
bowtie2	biology/bowtie2: fix build on powerpc64*	2022-11-09 23:50:41 +01:00
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape	biology/cytoscape: Fix build	2022-11-26 11:37:22 -08:00
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastq-trim
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes
garlic
gatk	biology/gatk: Update 4.2.6.1 -> 4.3.0.0	2022-11-26 20:06:47 -08:00
gcta
gemma
generand
gff2ps
gffread
gmap
gperiodic
graphlan
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy
igv
infernal
iolib
iqtree
jalview
jellyfish
kallisto
kmcp
lamarc
libbigwig
libcombine	biology/libcombine: Update 0.2.19 -> 0.2.20	2022-12-08 03:11:24 -08:00
libgff
libgtextutils
libneurosim
libnuml
libsbml
libsedml
linux-foldingathome
mafft
mapm3
megahit	biology/megahit: Add cmake patch to respect ports build flags	2022-11-24 08:10:13 -06:00
metaeuk	biology/metaeuk: Broken on systems where OpenMP isn't enabled	2022-12-02 20:00:49 -08:00
migrate
minimap2
mmseqs2
molden
mothur
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit	graphics/proj: Update to 9.1.0	2022-11-17 09:20:57 +01:00
ncbi-entrez-direct
ncbi-toolkit
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
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	biology/paml: Update to 4.10.6	2022-11-12 22:35:29 -04:00
pbbam
pbseqan
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	biology/py-biopython: Update to 1.80	2022-12-05 19:45:16 +08:00
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-libnuml
py-libsedml
py-loompy
py-macs2
py-mrcfile
py-multiqc
py-ont-fast5-api
py-orange3-bioinformatics	Revert: "all: deprecate ports depending on expired security/py-keyrings.alt"	2022-12-06 12:12:04 +01:00
py-orange3-single-cell	Revert: "all: deprecate ports depending on expired security/py-keyrings.alt"	2022-12-06 12:12:04 +01:00
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for genomes and metagenomes	2022-12-06 07:41:19 -08:00
py-pysam	biology/py-pysam: Update 0.19.1 -> 0.20.0	2022-11-10 09:36:45 -08:00
py-PySCeS
py-python-libsbml
py-pywgsim
py-resdk
py-scikit-bio
py-valerius
py-xenaPython
pyfasta
python-nexus
rainbow
rampler
readseq
recombine
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
sam2pairwise
samtools
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqio
seqkit
seqtk
sigviewer
sim4
slclust
smithwaterman
snpeff
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: Update 0.13.0 -> 0.14.0	2022-11-29 01:18:47 -08:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene
unikmer
vcf2hap
vcf-split
vcflib
vcftools
velvet
viennarna
vsearch
vt
wise
Makefile	biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for genomes and metagenomes	2022-12-06 07:41:19 -08:00