| .. |
|
abyss
|
cleanup: drop support for EOL FreeBSD 11.X
|
2021-09-30 23:23:30 +02:00 |
|
ad2vcf
|
biology/ad2vcf: Update to 0.1.3.31
|
2021-08-27 20:28:10 -05:00 |
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
biology/bamtools: Update to 2.5.2
|
2021-07-06 13:10:54 -05:00 |
|
bamutil
|
biology/bamutil: Utilities for working with SAM/BAM files
|
2021-10-12 11:40:35 -05:00 |
|
bbmap
|
biology/bbmap: Update to 38.92
|
2021-08-22 08:59:58 -05:00 |
|
bcftools
|
biology/bcftools: Update to 1.13
|
2021-07-12 08:30:10 -05:00 |
|
bedtools
|
|
|
|
bfc
|
biology/bfc: Correct sequencing errors from Illumina sequencing data
|
2021-08-23 12:28:41 -05:00 |
|
bioawk
|
|
|
|
biococoa
|
|
|
|
biolibc
|
biology/biolibc: Update to 0.2.0.11
|
2021-09-17 11:33:57 -05:00 |
|
biolibc-tools
|
biology/biolibc-tools: High-performance tools based on biolibc
|
2021-08-30 08:09:23 -05:00 |
|
bioparser
|
biology/bioparser: Update 3.0.12-2 -> 3.0.15
|
2021-09-21 09:41:49 -07:00 |
|
biosig
|
biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX
|
2021-08-16 19:57:30 -07:00 |
|
biosoup
|
|
|
|
biostar-tools
|
biology/biostar-tools: Add py-deeptools to metaport deps
|
2021-10-14 06:53:52 -05:00 |
|
bolt-lmm
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
biology/bowtie2: Update to 2.4.4
|
2021-05-24 11:35:43 -05:00 |
|
bwa
|
|
|
|
canu
|
|
|
|
cd-hit
|
biology/cd-hit: fix build on powerpc
|
2021-06-10 00:35:36 +00:00 |
|
cdbfasta
|
|
|
|
checkm
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
2021-05-10 22:13:20 +02:00 |
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
cufflinks
|
|
|
|
cytoscape
|
biology/cytoscape: mark unconditionally BROKEN
|
2021-05-12 14:55:52 +03:00 |
|
ddocent
|
cleanup: drop support for EOL FreeBSD 11.X
|
2021-09-30 23:23:30 +02:00 |
|
diamond
|
biology/diamond: Update to 2.0.12
|
2021-10-12 12:40:55 -03:00 |
|
dsr-pdb
|
|
|
|
edlib
|
biology/edlib: Update 1.2.6.20201202 -> 1.2.7
|
2021-08-21 10:12:15 -07:00 |
|
emboss
|
biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
|
2021-09-24 16:34:20 -05:00 |
|
erminej
|
biology/erminej: Analyses of gene sets, e.g. gene expression profiling
|
2021-07-09 07:26:58 -05:00 |
|
exonerate
|
|
|
|
fasta
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
fasta3
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
2021-05-06 13:47:41 +02:00 |
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
biology/fastp: Update to 0.22.0
|
2021-08-26 14:48:10 -05:00 |
|
fastqc
|
|
|
|
fasttree
|
biology/fasttree: fix build on armv7
|
2021-06-15 08:41:19 +00:00 |
|
fastx-toolkit
|
|
|
|
figtree
|
|
|
|
flash
|
biology/flash: Fast Length Adjustment of SHort reads
|
2021-08-23 12:26:47 -05:00 |
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
|
|
|
gatk
|
|
|
|
gcta
|
|
|
|
gemma
|
math/gsl: update to 2.7
|
2021-06-16 21:31:27 +02:00 |
|
generand
|
|
|
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
|
|
|
graphlan
|
|
|
|
groopm
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
2021-05-10 22:13:20 +02:00 |
|
haplohseq
|
|
|
|
hhsuite
|
biology/hhsuite: Fix build on aarch64
|
2021-09-13 17:47:57 +02:00 |
|
hisat2
|
|
|
|
hmmer
|
|
|
|
htslib
|
biology/htslib: Add CPE information
|
2021-09-10 21:18:20 +00:00 |
|
hyphy
|
biology/hyphy: Enable on aarch64.
|
2021-10-08 18:27:33 +02:00 |
|
igv
|
cleanup: drop support for EOL FreeBSD 11.X
|
2021-09-30 23:23:30 +02:00 |
|
infernal
|
|
|
|
iolib
|
biology/iolib: Drop maintainership
|
2021-05-19 20:56:24 +01:00 |
|
iqtree
|
|
|
|
jalview
|
cleanup: drop support for EOL FreeBSD 11.X
|
2021-09-30 23:23:30 +02:00 |
|
jellyfish
|
*: Clean up some things
|
2021-10-12 17:01:38 +02:00 |
|
kallisto
|
|
|
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgtextutils
|
|
|
|
libneurosim
|
biology/libneurosim: New port: Common interfaces for neuronal simulators
|
2021-10-08 10:20:27 -07:00 |
|
libnuml
|
biology/libnuml: New port: C++ library for Numerical Markup Language
|
2021-09-18 23:47:02 -07:00 |
|
libsbml
|
biology/libsbml: Rename LIBXML option to LIBXML2
|
2021-05-12 05:46:56 +08:00 |
|
libsedml
|
biology/libsedml: New port: C++ SED-ML library
|
2021-09-19 11:15:35 -07:00 |
|
linux-foldingathome
|
biology/linux-foldingathome: Update to 7.6.21
|
2021-06-25 19:13:19 +02:00 |
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
biology/minimap2: Add pkg-plist to repo
|
2021-08-22 12:46:37 -05:00 |
|
mmseqs2
|
biology/mmseqs2: disable on 32-bits
|
2021-09-12 21:05:53 +00:00 |
|
molden
|
graphics/mesa-libs: Bump reverse deps for libglvnd
|
2021-06-22 11:53:08 -07:00 |
|
mopac
|
|
|
|
mothur
|
biology/mothur: Update 1.46.0 -> 1.46.1
|
2021-09-02 02:29:56 -07:00 |
|
mrbayes
|
*: Remove unnecessary 'port' argument from USES=readline
|
2021-05-15 09:14:04 +02:00 |
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
biology/ncbi-blast+: Update to 2.12.0
|
2021-07-02 11:48:20 -05:00 |
|
ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0
|
2021-10-01 00:14:37 -07:00 |
|
ncbi-entrez-direct
|
biology/ncbi-entrez-direct: Update to 14.9.20210423_1
|
2021-04-26 11:53:11 -05:00 |
|
ncbi-toolkit
|
|
|
|
ncbi-vdb
|
devel/libepoll-shim: update to 0.0.20210418
|
2021-04-26 14:17:32 +00:00 |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.11.0-> 2.11.1
|
2021-08-18 10:17:44 -07:00 |
|
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 1.7.7
|
2021-07-06 22:56:10 +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
|
*: fix tab vs. space issues, and comments according to the guide.
|
2021-10-16 11:51:39 +02:00 |
|
pbseqan
|
*: fix tab vs. space issues, and comments according to the guide.
|
2021-10-16 11:51:39 +02:00 |
|
peak-classifier
|
biology/peak-classifier: Update to 0.1.1.21
|
2021-09-02 18:15:40 -05:00 |
|
pear-merger
|
|
|
|
phrap
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phred
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phyml
|
Clean up some things
|
2021-04-15 10:31:56 +02:00 |
|
picard-tools
|
|
|
|
plink
|
|
|
|
pooler
|
biology/pooler: fix build on powerpc
|
2021-10-06 20:52:30 +00:00 |
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-biom-format
|
|
|
|
py-biopython
|
biology/py-biopython: Update to 1.79
|
2021-10-12 14:43:04 +08:00 |
|
py-bx-python
|
biology/py-bx-python: Update 0.8.10 -> 0.8.11-6
|
2021-08-17 12:10:45 -07:00 |
|
py-crossmap
|
biology/py-crossmap: chase ad5a0604c4
|
2021-10-14 00:53:16 +00:00 |
|
py-cutadapt
|
biology/py-cutadapt: Update strict py-dnaio dep version
|
2021-05-04 08:20:39 -05:00 |
|
py-deeptools
|
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
|
2021-10-14 06:51:12 -05:00 |
|
py-deeptoolsintervals
|
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
|
2021-10-13 11:02:13 -05:00 |
|
py-dnaio
|
biology/py-dnaio: Update to 0.5.1
|
2021-05-04 08:19:25 -05:00 |
|
py-ete3
|
|
|
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
|
|
|
py-goatools
|
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
|
2021-07-02 12:00:29 -05:00 |
|
py-gtfparse
|
|
|
|
py-hits
|
|
|
|
py-libnuml
|
biology/py-libnuml: Fix typo
|
2021-09-19 11:15:35 -07:00 |
|
py-libsedml
|
biology/py-libsedml: New port: SED-ML library for Python
|
2021-09-19 11:15:36 -07:00 |
|
py-loompy
|
|
|
|
py-macs2
|
|
|
|
py-multiqc
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
2021-05-10 22:13:20 +02:00 |
|
py-ont-fast5-api
|
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
|
2021-08-13 08:34:09 -05:00 |
|
py-orange3-bioinformatics
|
biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1
|
2021-04-27 01:56:19 -07:00 |
|
py-orange3-single-cell
|
|
|
|
py-pandas-charm
|
|
|
|
py-py2bit
|
biology/py-py2bit: Python interface for 2bit packed nucleotide files
|
2021-10-13 07:53:53 -05:00 |
|
py-pybigwig
|
biology/py-bigwig: Rename to biology/py-pybigwig
|
2021-10-13 16:21:32 -05:00 |
|
py-pyfaidx
|
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5
|
2021-04-23 14:57:50 -07:00 |
|
py-pysam
|
|
|
|
py-PySCeS
|
biology/py-PySCeS: Update 0.9.8a -> 1.0.0
|
2021-09-20 14:34:22 -07:00 |
|
py-python-libsbml
|
biology/py-python-libsbml: New port: LibSBML Python API
|
2021-08-17 14:30:07 -07:00 |
|
py-pywgsim
|
biology/py-pywgsim: Modified wgsim genomic data simulator
|
2021-09-06 07:55:49 -05:00 |
|
py-resdk
|
biology/py-resdk: Update 13.3.0 -> 13.4.0
|
2021-08-17 10:29:42 -07:00 |
|
py-scikit-bio
|
|
|
|
py-xenaPython
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
rampler
|
|
|
|
readseq
|
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
|
2021-04-18 09:20:28 -05:00 |
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
biology/rubygem-bio: Update to 2.0.2
|
2021-07-01 04:44:06 +08:00 |
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
|
|
rubygem-bio-shell
|
|
|
|
sam2pairwise
|
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
|
2021-09-07 15:32:29 -05:00 |
|
samtools
|
biology/samtools: Update to 1.13
|
2021-07-12 08:24:26 -05:00 |
|
scrm
|
|
|
|
seaview
|
biology/seaview: in preparation to FLTK update, unbreak the port
|
2021-08-14 08:58:03 +00:00 |
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan3
|
biology/seqan3: Add the 'test' target (currently broken due to lacking clang support)
|
2021-08-13 10:08:56 -07:00 |
|
seqan-apps
|
*/*: Remove compiler:openmp from Mk/Uses/compiler.mk
|
2021-10-03 19:47:27 +02:00 |
|
seqio
|
|
|
|
seqkit
|
biology/seqkit: Update 0.16.1 -> 2.0.1
|
2021-09-18 10:48:26 -07:00 |
|
seqtk
|
|
|
|
sigviewer
|
misc/: Update 0.99.6-2 -> 0.991
|
2021-08-18 10:17:45 -07:00 |
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
biology/snpeff: Improvements to Makefile and patches
|
2021-04-19 11:41:58 -05:00 |
|
spoa
|
|
|
|
sra-tools
|
biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives
|
2021-06-22 12:55:15 -05:00 |
|
stacks
|
|
|
|
star
|
|
|
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit
|
2021-05-26 15:25:22 -07:00 |
|
treekin
|
biology/treekin: Unbreak
|
2021-10-15 08:50:24 -07:00 |
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ucsc-userapps
|
biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin
|
2021-09-24 16:53:30 -05:00 |
|
ugene
|
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
|
2021-10-14 11:23:37 +00:00 |
|
unikmer
|
biology/unikmer: Update 0.18.4 -> 0.18.8
|
2021-09-26 01:54:07 -07:00 |
|
vcf2hap
|
biology/vcf2hap: Update to 0.1.3.12
|
2021-08-27 20:32:51 -05:00 |
|
vcf-split
|
biology/vcf-split: Update to 0.1.2.14
|
2021-08-27 20:30:52 -05:00 |
|
vcflib
|
|
|
|
vcftools
|
biology/vcftools: Add CPE information
|
2021-09-25 20:28:38 +00:00 |
|
velvet
|
|
|
|
viennarna
|
math/gsl: update to 2.7
|
2021-06-16 21:31:27 +02:00 |
|
vsearch
|
biology/vsearch: Update to 2.17.1
|
2021-06-19 07:33:58 -05:00 |
|
vt
|
|
|
|
wise
|
|
|
|
Makefile
|
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
|
2021-10-14 06:51:12 -05:00 |
