| .. |
|
abyss
|
cleanup: drop support for EOL FreeBSD 11.X
|
11 months ago |
|
ad2vcf
|
biology/ad2vcf: Update to 0.1.4
|
8 months ago |
|
artemis
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
avida
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
babel
|
*/*: Remove redundant '-*' from CONFLICTS definitions
|
9 months ago |
|
bamtools
|
devel/jsoncpp: Update to 1.9.4 -> 1.9.5
|
9 months ago |
|
bamutil
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
bbmap
|
biology/bbmap: Update to 38.92
|
12 months ago |
|
bcftools
|
math/gsl: bump portrevision of consumers after update to 2.7.1
|
7 months ago |
|
bedtools
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
bfc
|
biology/bfc: Correct sequencing errors from Illumina sequencing data
|
12 months ago |
|
bio-mocha
|
biology/bio-mocha: Update to 1.14-20220112
|
7 months ago |
|
bioawk
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
biococoa
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
biolibc
|
biology/biolibc: Update to 0.2.1
|
8 months ago |
|
biolibc-tools
|
biology/biolibc-tools: Update to 0.1.1
|
8 months ago |
|
bioparser
|
biology/bioparser: Update 3.0.12-2 -> 3.0.15
|
11 months ago |
|
biosig
|
biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX
|
1 year ago |
|
biosoup
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
biostar-tools
|
biology/biostar-tools: Allow package build on non-amd64 systems
|
8 months ago |
|
bolt-lmm
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
bowtie
|
biology/bowtie: enable on riscv64
|
8 months ago |
|
bowtie2
|
biology/bowtie2: Update to 2.4.5
|
7 months ago |
|
bwa
|
biology/bwa: don't use GCC on powerpc64le
|
8 months ago |
|
canu
|
biology/canu: fix CATEGORIES
|
8 months ago |
|
cd-hit
|
biology/cd-hit: fix build on armv7
|
9 months ago |
|
cdbfasta
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
checkm
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
1 year ago |
|
clustal-omega
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
clustalw
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
cufflinks
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
cytoscape
|
biology/cytoscape: mark unconditionally BROKEN
|
1 year ago |
|
ddocent
|
cleanup: drop support for EOL FreeBSD 11.X
|
11 months ago |
|
diamond
|
biology/diamond: Update to 2.0.14
|
7 months ago |
|
dsr-pdb
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
edlib
|
biology/edlib: Update 1.2.6.20201202 -> 1.2.7
|
12 months ago |
|
emboss
|
*/*: Remove redundant '-[0-9]*' from CONFLICTS
|
10 months ago |
|
erminej
|
biology/erminej: Analyses of gene sets, e.g. gene expression profiling
|
1 year ago |
|
exonerate
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
fasta
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
fasta3
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
1 year ago |
|
fastahack
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
fastdnaml
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
fastool
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
fastp
|
biology/fastp: Add USE_GCC to hack around seg faults
|
7 months ago |
|
fastqc
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
fasttree
|
biology/fasttree: fix build on armv7
|
1 year ago |
|
fastx-toolkit
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
figtree
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
flash
|
biology/flash: Fast Length Adjustment of SHort reads
|
12 months ago |
|
fluctuate
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
freebayes
|
biology/freebayes: enable on riscv64
|
8 months ago |
|
garlic
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
gatk
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
gcta
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
gemma
|
math/gsl: bump portrevision of consumers after update to 2.7.1
|
7 months ago |
|
generand
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
gff2ps
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
gffread
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
gmap
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
gperiodic
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
graphlan
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
groopm
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
1 year ago |
|
haplohseq
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
hhsuite
|
biology/hhsuite: fix packaging on powerpc
|
9 months ago |
|
hisat2
|
biology/hisat2: enable on riscv64
|
8 months ago |
|
hmmer
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
htslib
|
biology/htslib: Update to 1.14
|
8 months ago |
|
hyphy
|
biology/hyphy: Update to 2.5.33
|
9 months ago |
|
igv
|
cleanup: drop support for EOL FreeBSD 11.X
|
11 months ago |
|
infernal
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
iolib
|
biology/iolib: Drop maintainership
|
1 year ago |
|
iqtree
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
jalview
|
cleanup: drop support for EOL FreeBSD 11.X
|
11 months ago |
|
jellyfish
|
*: Clean up some things
|
10 months ago |
|
kallisto
|
biology/kallisto: Update to 0.48.0
|
7 months ago |
|
lamarc
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
libbigwig
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
libgff
|
biology/libgff: GFF/GTF parsing library based on GCLib
|
8 months ago |
|
libgtextutils
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
libneurosim
|
biology/libneurosim: New port: Common interfaces for neuronal simulators
|
10 months ago |
|
libnuml
|
biology/libnuml: New port: C++ library for Numerical Markup Language
|
11 months ago |
|
libsbml
|
biology/libsbml: Fix build with Python 3.10
|
9 months ago |
|
libsedml
|
biology/libsedml: New port: C++ SED-ML library
|
11 months ago |
|
linux-foldingathome
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
10 months ago |
|
mafft
|
biology/mafft: Update to 7.267
|
10 months ago |
|
mapm3
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
migrate
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
minimap2
|
biology/minimap2: Update to 2.24
|
7 months ago |
|
mmseqs2
|
biology/mmseqs2: disable on 32-bits
|
11 months ago |
|
molden
|
*: Clean up some things
|
7 months ago |
|
mopac
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
mothur
|
biology/mothur: Update 1.46.1 -> 1.47.0
|
7 months ago |
|
mrbayes
|
*: Remove unnecessary 'port' argument from USES=readline
|
1 year ago |
|
mummer
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
muscle
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
ncbi-blast+
|
biology/ncbi-blast+: fix build on powerpc
|
7 months ago |
|
ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Update 25.2.0 -> 26.0.1
|
7 months ago |
|
ncbi-entrez-direct
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
ncbi-toolkit
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
ncbi-vdb
|
security/mbedtls: Update to 2.28.0 and fix make test
|
7 months ago |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.11.1 -> 2.11.2
|
7 months ago |
|
p5-AcePerl
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-ASN1-EntrezGene
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Cluster
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Coordinate
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-DB-EMBL
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-DB-NCBIHelper
|
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7
|
1 year ago |
|
p5-Bio-Das
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Das-Lite
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-FeatureIO
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-GFF3
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Glite
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Graphics
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-MAGETAB
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-NEXUS
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Phylo
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-SCF
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-Bio-Variation
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-BioPerl
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-BioPerl-Run
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
p5-TrimGalore
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
p5-transdecoder
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
paml
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
pbbam
|
*: fix tab vs. space issues, and comments according to the guide.
|
10 months ago |
|
pbseqan
|
*: fix tab vs. space issues, and comments according to the guide.
|
10 months ago |
|
peak-classifier
|
biology/peak-classifier: Update to 0.1.2
|
8 months ago |
|
pear-merger
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
phrap
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
1 year ago |
|
phred
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
1 year ago |
|
phyml
|
biology/phyml: update to 3.3.20211231
|
7 months ago |
|
picard-tools
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
plink
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
pooler
|
biology/pooler: fix build on powerpc
|
10 months ago |
|
primer3
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
prodigal
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
prodigy-lig
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
protomol
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
psi88
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
py-Genesis-PyAPI
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-PySCeS
|
biology/py-PySCeS: Update 0.9.8a -> 1.0.0
|
11 months ago |
|
py-biom-format
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-biopython
|
biology/py-biopython: Update to 1.79
|
10 months ago |
|
py-bx-python
|
biology/py-bx-python: Update 0.8.11-6 -> 0.8.13
|
8 months ago |
|
py-crossmap
|
biology/py-crossmap: chase ad5a0604c4
|
10 months ago |
|
py-cutadapt
|
biology/py-cutadapt: Update strict py-dnaio dep version
|
1 year ago |
|
py-deeptools
|
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
|
10 months ago |
|
py-deeptoolsintervals
|
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
|
10 months ago |
|
py-dnaio
|
biology/py-dnaio: Update to 0.5.1
|
1 year ago |
|
py-ete3
|
PyQt: Update sip to 6.5.0, reintroduce sip4 and simplify PyQt framework.
|
7 months ago |
|
py-gffutils
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-goatools
|
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
|
1 year ago |
|
py-gtfparse
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-hits
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-libnuml
|
biology/py-libnuml: fix install with python 3.10+
|
9 months ago |
|
py-libsedml
|
biology/py-libsedml: fix install with python 3.10+
|
9 months ago |
|
py-loompy
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-macs2
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-multiqc
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
1 year ago |
|
py-ont-fast5-api
|
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
|
1 year ago |
|
py-orange3-bioinformatics
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
7 months ago |
|
py-orange3-single-cell
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
7 months ago |
|
py-pandas-charm
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-py2bit
|
biology/py-py2bit: Python interface for 2bit packed nucleotide files
|
10 months ago |
|
py-pybigwig
|
biology/py-bigwig: Rename to biology/py-pybigwig
|
10 months ago |
|
py-pyfaidx
|
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5
|
1 year ago |
|
py-pysam
|
biology/py-pysam: Update 0.16.0.1 -> 0.18.0
|
8 months ago |
|
py-python-libsbml
|
biology/py-python-libsbml: limit supported python versions, fix build
|
9 months ago |
|
py-pywgsim
|
biology/py-pywgsim: Modified wgsim genomic data simulator
|
11 months ago |
|
py-resdk
|
biology/py-resdk: Update 13.8.0 -> 14.0.0
|
7 months ago |
|
py-scikit-bio
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
py-xenaPython
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
pyfasta
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
python-nexus
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
rainbow
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
rampler
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
readseq
|
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
|
1 year ago |
|
recombine
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
ruby-bio
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
rubygem-bio
|
biology/rubygem-bio: Update to 2.0.3
|
7 months ago |
|
rubygem-bio-executables
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
rubygem-bio-old-biofetch-emulator
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
rubygem-bio-shell
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
sam2pairwise
|
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
|
11 months ago |
|
samtools
|
biology/samtools: Update to 1.14
|
8 months ago |
|
scrm
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
seaview
|
biology/seaview: Update version 5.0.4=>5.0.5
|
8 months ago |
|
seqan
|
*/*: Remove redundant '-[0-9]*' from CONFLICTS
|
10 months ago |
|
seqan-apps
|
*/*: Remove compiler:openmp from Mk/Uses/compiler.mk
|
10 months ago |
|
seqan1
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
seqan3
|
biology/seqan3: Update 3.0.3 -> 3.1.0
|
9 months ago |
|
seqio
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
seqkit
|
biology/seqkit: Update 2.0.1 -> 2.1.0
|
9 months ago |
|
seqtk
|
biology/seqtk: Update to 1.3
|
8 months ago |
|
sigviewer
|
misc/: Update 0.99.6-2 -> 0.991
|
12 months ago |
|
sim4
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
slclust
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
smithwaterman
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
snpeff
|
biology/snpeff: Improvements to Makefile and patches
|
1 year ago |
|
spoa
|
devel/cpu_features: Install cmake files, install headers into a dedicated directory
|
7 months ago |
|
sra-tools
|
Fix CONFLICTS entries of multiple ports
|
7 months ago |
|
stacks
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
star
|
biology/star: Update to 2.7.9a
|
9 months ago |
|
stringtie
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
subread
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
tRNAscan-SE
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
tabixpp
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
taxonkit
|
biology/taxonkit: Update 0.8.0 -> 0.9.0
|
8 months ago |
|
treekin
|
biology/treekin: Unbreak
|
10 months ago |
|
treepuzzle
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
trimadap
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
10 months ago |
|
trimmomatic
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
ucsc-userapps
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
10 months ago |
|
ugene
|
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
|
10 months ago |
|
unikmer
|
biology/unikmer: Update 0.18.4 -> 0.18.8
|
11 months ago |
|
vcf-split
|
biology/vcf-split: Update to 0.1.3.3
|
8 months ago |
|
vcf2hap
|
biology/vcf2hap: Update to 0.1.4
|
8 months ago |
|
vcflib
|
biology/vcflib: Update to 1.0.3
|
7 months ago |
|
vcftools
|
biology/vcftools: Add CPE information
|
11 months ago |
|
velvet
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
viennarna
|
biology/viennarna: Update 2.4.18 -> 2.5.0
|
7 months ago |
|
vsearch
|
biology/vsearch: Update to 2.21.1
|
7 months ago |
|
vt
|
One more small cleanup, forgotten yesterday.
|
1 year ago |
|
wise
|
Remove # $FreeBSD$ from Makefiles.
|
1 year ago |
|
Makefile
|
biology/libgff: GFF/GTF parsing library based on GCLib
|
8 months ago |
Tijl Coosemans
b93e64d3c3