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freebsd-ports/biology
History
Yuri Victorovich fb0f71e5cc biology/unikmer: Update 0.18.1 -> 0.18.3 
Reported by:	portscout
2021-07-28 10:13:47 -07:00
..
abyss
biology/abyss: Update 2.3.0-3 -> 2.3.1
2021-04-22 10:18:02 -07:00
ad2vcf
biology/ad2vcf: Remove comment used to silence portlint
2021-06-11 10:39:02 -05:00
artemis
…
avida
…
babel
…
bamtools
biology/bamtools: Update to 2.5.2
2021-07-06 13:10:54 -05:00
bbmap
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
2021-04-18 11:21:29 -05:00
bcftools
biology/bcftools: Update to 1.13
2021-07-12 08:30:10 -05:00
bedtools
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
bioawk
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
biococoa
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
biolibc
biology/biolibc: Remove comment used to silence portlint
2021-06-11 10:38:27 -05:00
bioparser
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
biosoup
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
biostar-tools
biology/biostar-tools: Add erminej run depend to metaport
2021-07-09 07:35:55 -05:00
bolt-lmm
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
bowtie
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
bowtie2
biology/bowtie2: Update to 2.4.4
2021-05-24 11:35:43 -05:00
bwa
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
canu
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
clustalw
…
cufflinks
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
cytoscape
biology/cytoscape: mark unconditionally BROKEN
2021-05-12 14:55:52 +03:00
ddocent
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
diamond
biology/diamond: Update to 2.0.11-1
2021-07-06 10:15:24 -03:00
dsr-pdb
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
edlib
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
emboss
…
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fastdnaml
…
fastool
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fastp
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fastqc
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fasttree
biology/fasttree: fix build on armv7
2021-06-15 08:41:19 +00:00
fastx-toolkit
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
figtree
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fluctuate
…
freebayes
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
garlic
…
gatk
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
gcta
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
gemma
math/gsl: update to 2.7
2021-06-16 21:31:27 +02:00
generand
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
gff2ps
…
gmap
…
gperiodic
…
graphlan
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
groopm
math/py-matplotlib: chase minimum Python version in dependent ports
2021-05-10 22:13:20 +02:00
haplohseq
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
hhsuite
biology/hhsuite: fix build on powerpc64*
2021-07-08 13:13:54 +00:00
hisat2
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
hmmer
…
htslib
htslib: Update to 1.13
2021-07-12 08:16:45 -05:00
hyphy
biology/hyphy: Update to 2.5.31
2021-06-05 20:00:24 -03:00
igv
biology/igv: Fix build
2021-06-27 05:33:51 -04:00
infernal
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
iolib
biology/iolib: Drop maintainership
2021-05-19 20:56:24 +01:00
iqtree
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
jalview
biology/jalview: Fix build
2021-06-27 05:30:39 -04:00
jellyfish
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
kallisto
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
lamarc
…
libbigwig
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
libgtextutils
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
libsbml
biology/libsbml: Rename LIBXML option to LIBXML2
2021-05-12 05:46:56 +08:00
linux-foldingathome
biology/linux-foldingathome: Update to 7.6.21
2021-06-25 19:13:19 +02:00
mafft
…
mapm3
…
migrate
…
minimap2
biology/minimap2: Update to 2.20
2021-05-29 16:06:34 -05:00
mmseqs2
biology/mmseqs2: Fix runtime error when built with clang
2021-06-29 09:04:48 -05:00
molden
graphics/mesa-libs: Bump reverse deps for libglvnd
2021-06-22 11:53:08 -07:00
mopac
…
mothur
biology/mothur: Update 1.45.2 -> 1.45.3
2021-05-09 09:11:11 -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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH
2021-04-15 10:01:31 -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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
p5-TrimGalore
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
paml
…
pbbam
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
pbseqan
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
peak-classifier
biology/peak-classifier: Classify peaks based on GFF features
2021-06-14 11:40:33 -05:00
pear-merger
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
plink
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
pooler
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
primer3
…
prodigal
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
prodigy-lig
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
protomol
…
psi88
…
py-bigwig
biology/py-bigwig: Fix packaging with Python 3.8+
2021-04-21 09:41:29 +02:00
py-biom-format
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-biopython
…
py-bx-python
…
py-crossmap
biology/py-crossmap: Update to 0.5.4
2021-04-21 08:31:13 -05:00
py-cutadapt
biology/py-cutadapt: Update strict py-dnaio dep version
2021-05-04 08:20:39 -05:00
py-dnaio
biology/py-dnaio: Update to 0.5.1
2021-05-04 08:19:25 -05:00
py-ete3
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-gffutils
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-goatools
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
2021-07-02 12:00:29 -05:00
py-gtfparse
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-hits
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-loompy
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-macs2
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-multiqc
math/py-matplotlib: chase minimum Python version in dependent ports
2021-05-10 22:13:20 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-pandas-charm
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-pyfaidx
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5
2021-04-23 14:57:50 -07:00
py-pysam
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-resdk
biology/py-resdk: Update 13.2.0 -> 13.3.0
2021-05-24 00:26:50 -07:00
py-scikit-bio
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
py-xenaPython
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
pyfasta
…
python-nexus
…
rainbow
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
rampler
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
…
samtools
biology/samtools: Update to 1.13
2021-07-12 08:24:26 -05:00
scrm
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
seaview
…
seqan
…
seqan1
…
seqan3
biology/seqan3: Update 3.0.2-1195 -> 3.0.3
2021-05-29 22:38:08 -07:00
seqan-apps
biology/seqan-apps: fix packaging on armv7
2021-06-21 08:11:25 +00:00
seqio
…
seqkit
biology/seqkit: Update 0.16.0 -> 0.16.1
2021-05-19 23:02:26 -07:00
seqtk
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
sim4
…
slclust
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
smithwaterman
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
snpeff
biology/snpeff: Improvements to Makefile and patches
2021-04-19 11:41:58 -05:00
spoa
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
star
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
stringtie
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
subread
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
tabixpp
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
taxonkit
biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit
2021-05-26 15:25:22 -07:00
treekin
math/lapack: +math/blas et al., upgrade to 3.9.1
2021-06-13 19:48:12 +02:00
treepuzzle
…
trimadap
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
trimmomatic
…
tRNAscan-SE
…
ucsc-userapps
biology/ucsc-userapps: Update to v414
2021-05-15 10:23:08 -05:00
ugene
biology/ugene: update Unipro UGENE to version 39.0.
2021-06-25 17:56:47 +00:00
unikmer
biology/unikmer: Update 0.18.1 -> 0.18.3
2021-07-28 10:13:47 -07:00
vcf2hap
biology/vcf2hap: Remove comment used to silence portlint
2021-06-11 10:40:11 -05:00
vcf-split
biology/vcf-split: Update to 0.1.2
2021-06-11 10:05:19 -05:00
vcflib
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
vcftools
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
wise
…
Makefile
biology/erminej: Analyses of gene sets, e.g. gene expression profiling
2021-07-09 07:26:58 -05:00