| .. |
|
abyss
|
|
|
|
ad2vcf
|
|
|
|
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
|
|
|
|
bedtools
|
|
|
|
bfc
|
|
|
|
bifrost
|
|
|
|
bio-mocha
|
|
|
|
bioawk
|
|
|
|
biococoa
|
|
|
|
biolibc
|
biology/biolibc: Impelled to share/man
|
2024-01-23 15:51:25 +01:00 |
|
biolibc-tools
|
|
|
|
bioparser
|
|
|
|
biosig
|
*/*: bump PORTREVISION after the upgrade to SuiteSparse
|
2024-01-28 13:02:23 +01:00 |
|
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
|
|
|
|
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
|
|
|
|
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
|
|
|
|
gemma
|
|
|
|
generand
|
|
|
|
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
|
|
|
|
kallisto
|
|
|
|
kmcp
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
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: Fix build on 14.x and main
|
2023-12-13 23:11:55 -08:00 |
|
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
|
MAN[1-5]PREFIX: eleminate its usage and move man to share/man
|
2024-01-09 16:41:04 +01:00 |
|
minimap2
|
|
|
|
mmseqs2
|
|
|
|
molden
|
|
|
|
mothur
|
|
|
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
devel/grpc: Update to 1.61.1
|
2024-02-21 23:06:22 +08:00 |
|
ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Broken on armv7
|
2024-01-20 20:09:20 -08:00 |
|
ncbi-entrez-direct
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
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
|
|
|
|
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
|
|
|
|
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
|
biology/py-cutadapt: Update to 4.6
|
2024-02-06 06:55:32 -06:00 |
|
py-deeptools
|
|
|
|
py-deeptoolsintervals
|
|
|
|
py-dna-features-viewer
|
|
|
|
py-dnaio
|
biology/py-dnaio: Update to 1.2.0
|
2024-02-06 06:51:39 -06:00 |
|
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: Peak caller for TF binding sites
|
2024-01-10 09:19:56 -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
|
|
|
|
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 3.2.1 → 3.2.2
|
2024-01-21 01:44:54 -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
|
|
|
|
py-pywgsim
|
|
|
|
py-resdk
|
|
|
|
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
|
|
|
|
scrm
|
|
|
|
seaview
|
MANPREFIX: eliminate its usage
|
2024-01-12 16:11:29 +01:00 |
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan3
|
|
|
|
seqan-apps
|
|
|
|
seqkit
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
seqtk
|
|
|
|
seqwish
|
|
|
|
sigviewer
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
|
|
|
spoa
|
|
|
|
sra-tools
|
|
|
|
stacks
|
|
|
|
star
|
|
|
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
treekin
|
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
|
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
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
vcf2hap
|
|
|
|
vcf-split
|
|
|
|
vcflib
|
lang/zig: update to 0.11.0
|
2024-01-01 06:37:19 +01:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
|
vsearch
|
biology/vsearch: Update to 2.27.0
|
2024-01-23 07:16:13 -06:00 |
|
vt
|
|
|
|
wfa2-lib
|
|
|
|
wise
|
|
|
|
Makefile
|
biology/py-newick: Add new port
|
2024-02-03 00:58:29 +00:00 |
