Yuri Victorovich e8e22bb84f biology/seqan3: Update 3.0.3 -> 3.1.0 ... Reported by: portscout		2021-11-14 21:18:53 -08:00
..
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	devel/jsoncpp: Update to 1.9.4 -> 1.9.5	2021-11-05 12:09:19 -07:00
bamutil	biology/bamutil: Update to 1.0.15	2021-10-20 14:43:38 -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	biostar-tools: Add gffread to metaport deps	2021-11-10 14:52:01 -06:00
bolt-lmm
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape
ddocent	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
diamond	biology/diamond: Update to 2.0.13	2021-11-11 13:17:24 -04:00
dsr-pdb
edlib	biology/edlib: Update 1.2.6.20201202 -> 1.2.7	2021-08-21 10:12:15 -07:00
emboss	*/*: Remove redundant '-[0-9]*' from CONFLICTS	2021-10-29 11:50:18 +02:00
erminej
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Update to 0.23.1	2021-10-20 11:37:39 -05:00
fastqc
fasttree
fastx-toolkit
figtree
flash	biology/flash: Fast Length Adjustment of SHort reads	2021-08-23 12:26:47 -05:00
fluctuate
freebayes	biology/freebayes: builds fine on armv7	2021-11-05 01:14:22 +00:00
garlic
gatk
gcta
gemma
generand
gff2ps
gffread	biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc	2021-11-10 14:49:10 -06:00
gmap	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
gperiodic
graphlan
groopm
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 armv7	2021-11-12 14:48:47 +00:00
igv	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
infernal
iolib
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: Fix build with Python 3.10	2021-11-02 05:28:40 +08:00
libsedml	biology/libsedml: New port: C++ SED-ML library	2021-09-19 11:15:35 -07:00
linux-foldingathome	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
mafft	biology/mafft: Update to 7.267	2021-10-22 13:11:23 +08:00
mapm3
migrate
minimap2	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
mmseqs2	biology/mmseqs2: disable on 32-bits	2021-09-12 21:05:53 +00:00
molden
mopac
mothur	biology/mothur: Update 1.46.0 -> 1.46.1	2021-09-02 02:29:56 -07:00
mrbayes
mummer
muscle
ncbi-blast+	devel/grpc: Update to 1.41.0	2021-10-25 23:57:13 +08:00
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
ncbi-toolkit
ncbi-vdb
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
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
phred
phyml
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
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
py-ete3
py-Genesis-PyAPI
py-gffutils
py-goatools
py-gtfparse
py-hits
py-libnuml	biology/py-libnuml: fix install with python 3.10+	2021-11-02 21:08:32 +03:00
py-libsedml	biology/py-libsedml: fix install with python 3.10+	2021-11-02 21:08:31 +03:00
py-loompy
py-macs2
py-multiqc
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
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
py-pysam	biology/py-pysam: limit supported python versions	2021-11-01 16:59:09 +03:00
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: limit supported python versions, fix build	2021-11-03 21:26:41 +03:00
py-pywgsim	biology/py-pywgsim: Modified wgsim genomic data simulator	2021-09-06 07:55:49 -05:00
py-resdk	biology/py-resdk: Update 13.4.0 -> 13.6.0	2021-10-22 01:57:04 -07:00
py-scikit-bio
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	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	*/*: Remove redundant '-[0-9]*' from CONFLICTS	2021-10-29 11:50:18 +02:00
seqan1
seqan3	biology/seqan3: Update 3.0.3 -> 3.1.0	2021-11-14 21:18:53 -08:00
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
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit
treekin	biology/treekin: Unbreak	2021-10-15 08:50:24 -07:00
treepuzzle
trimadap	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
trimmomatic
tRNAscan-SE
ucsc-userapps	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
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	biology/vcflib: Update to 1.0.2	2021-11-04 09:23:17 -05:00
vcftools	biology/vcftools: Add CPE information	2021-09-25 20:28:38 +00:00
velvet
viennarna
vsearch	Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)	2021-10-25 12:58:29 +00:00
vt
wise
Makefile	biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc	2021-11-10 14:49:10 -06:00