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Tijl Coosemans b93e64d3c3 security/mbedtls: Update to 2.28.0 and fix make test 7 months ago
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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