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freebsd-ports/biology
History
Yuri Victorovich 44210d2f50 biology/seqkit: Update 2.1.0 -> 2.2.0 
Reported by:	portscout
2022-04-19 20:44:55 -07:00
..
abyss
cleanup: drop support for EOL FreeBSD 11.X
2021-09-30 23:23:30 +02:00
ad2vcf
biology/ad2vcf: Update to 0.1.5
2022-03-15 16:39:32 -05:00
artemis
…
avida
…
babel
*/*: Remove redundant '-*' from CONFLICTS definitions
2021-11-25 22:40:11 +01:00
bamtools
devel/jsoncpp: Update to 1.9.4 -> 1.9.5
2021-11-05 12:09:19 -07:00
bamutil
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
bbmap
biology/bbmap: Update to 38.92
2021-08-22 08:59:58 -05:00
bcftools
biology/bcftools: Update to 1.15
2022-02-26 09:04:10 -06:00
bedtools
…
bfc
biology/bfc: Correct sequencing errors from Illumina sequencing data
2021-08-23 12:28:41 -05:00
bio-mocha
biology/bio-mocha: Update bcftools submodule to 1.15
2022-02-26 09:04:10 -06:00
bioawk
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biococoa
…
biolibc
biology/biolibc: Update to 0.2.2
2022-03-15 16:35:22 -05:00
biolibc-tools
biology/biolibc-tools: Update to 0.1.2
2022-03-15 16:36:49 -05:00
bioparser
biology/bioparser: Update 3.0.12-2 -> 3.0.15
2021-09-21 09:41:49 -07:00
biosig
biology/biosig: Update 2.3.3 -> 2.4.0
2022-03-20 12:43:56 -07:00
biosoup
…
biostar-tools
biology/biostar-tools: Allow package build on non-amd64 systems
2021-12-01 09:49:28 -06:00
bolt-lmm
biology/bolt-lmm: remove unnecessary flags for powerpc64le
2022-04-17 13:05:53 +02:00
bowtie
biology/bowtie: enable on riscv64
2021-12-15 13:55:57 +01:00
bowtie2
biology/bowtie2: Update to 2.4.5
2022-01-21 08:33:54 -06:00
bwa
biology/bwa: don't use GCC on powerpc64le
2021-12-01 17:34:18 +00:00
canu
biology/canu: fix CATEGORIES
2021-12-20 12:59:13 +00:00
cd-hit
biology/cd-hit: fix build on armv7
2021-11-21 13:26:44 +00:00
cdbfasta
…
checkm
biology/checkm: Update 1.1.8 -> 1.1.9
2022-04-15 12:09:58 -07:00
clustal-omega
…
clustalw
…
cufflinks
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
cytoscape
…
ddocent
cleanup: drop support for EOL FreeBSD 11.X
2021-09-30 23:23:30 +02:00
diamond
biology/diamond: Update to 2.0.14
2022-01-13 13:42:38 -04:00
dsr-pdb
biology/dsr-pdb: Remove -pg (mcount instrumentation) flag
2022-03-21 17:07:11 -07:00
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
biology/erminej: Analyses of gene sets, e.g. gene expression profiling
2021-07-09 07:26:58 -05:00
exonerate
…
fasta
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
fasta3
…
fastahack
…
fastdnaml
…
fastool
…
fastp
biology/fastp: Add USE_GCC to hack around seg faults
2022-01-21 10:16:01 -06:00
fastq-trim
biology/fastq-trim: Update to 0.1.1.4
2022-03-21 16:19:36 -05:00
fastqc
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fasttree
biology/fasttree: fix build on armv7
2021-06-15 08:41:19 +00:00
fastx-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
figtree
…
flash
biology/flash: Fast Length Adjustment of SHort reads
2021-08-23 12:26:47 -05:00
fluctuate
…
freebayes
biology/freebayes: Update to 1.3.6
2022-02-06 14:23:45 -06:00
garlic
…
gatk
biology/gatk: Update 4.2.0.0 -> 4.2.6.0
2022-04-10 16:21:50 -07:00
gcta
…
gemma
math/gsl: bump portrevision of consumers after update to 2.7.1
2022-01-12 20:41:22 +01:00
generand
…
gff2ps
…
gffread
biology/gffread: remove local poudriere files
2022-03-07 23:44:38 +01:00
gmap
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
gperiodic
…
graphlan
…
groopm
biology/groopm: Fix build with setuptools 58.0.0+
2022-03-25 21:38:04 +08:00
haplohseq
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hhsuite
biology/hhsuite: fix packaging on powerpc
2021-11-16 12:03:42 +00:00
hisat2
biology/hisat2: enable on riscv64
2021-12-16 22:38:56 +01:00
hmmer
…
htslib
biology/htslib: Update to 1.15
2022-02-26 09:04:10 -06:00
hyphy
biology/hyphy: Fix build with clang 13.0.0
2022-02-21 16:13:16 -04:00
igv
cleanup: drop support for EOL FreeBSD 11.X
2021-09-30 23:23:30 +02:00
infernal
*/*: fix trailing whitespace in pkg-descr's
2022-04-01 18:09:49 +03:00
iolib
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +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
biology/kallisto: Update to 0.48.0
2022-01-19 07:57:36 -06:00
lamarc
…
libbigwig
…
libgff
biology/libgff: GFF/GTF parsing library based on GCLib
2021-12-05 14:50:42 -06:00
libgtextutils
…
libneurosim
biology/libneurosim: New port: Common interfaces for neuronal simulators
2021-10-08 10:20:27 -07:00
libnuml
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
libsbml
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
libsedml
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
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
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
minimap2
biology/minimap2: Update to 2.24
2021-12-31 08:30:52 -06:00
mmseqs2
biology/mmseqs2: disable on 32-bits
2021-09-12 21:05:53 +00:00
molden
*: Clean up some things
2022-01-17 14:20:25 +01:00
mopac
…
mothur
biology/mothur: Update 1.46.1 -> 1.47.0
2022-01-21 09:14:38 -08:00
mrbayes
…
mummer
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
muscle
…
ncbi-blast+
devel/grpc: Update to 1.45.0
2022-03-31 06:02:45 +08:00
ncbi-cxx-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
ncbi-entrez-direct
*/*: Bump PORTREVISION after lang/go 1.18 update
2022-03-30 03:01:44 -04:00
ncbi-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
ncbi-vdb
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
ngs-sdk
biology/ngs-sdk: Update 2.11.1 -> 2.11.2
2022-01-27 01:29:09 -08:00
p5-AcePerl
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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 0.1.3
2022-03-15 16:41:51 -05:00
pear-merger
…
phrap
…
phred
…
phyml
biology/phyml: update to 3.3.20211231
2022-01-02 18:31:24 +01:00
picard-tools
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
plink
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
pooler
biology/pooler: Update to 1.84
2022-03-14 09:41:38 -05:00
primer3
…
prodigal
…
prodigy-lig
…
protomol
…
psi88
…
py-bcbio-gff
biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)
2022-02-03 13:38:42 -06:00
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 0.8.11-6 -> 0.8.13
2021-12-21 01:03:57 -08:00
py-crossmap
biology/py-crossmap: Fix build with setuptools 58.0.0+
2022-03-25 21:38:04 +08:00
py-cutadapt
biology/py-cutadapt: fix tests by adding missing test depend
2022-04-07 21:59:32 +03:00
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-dna-features-viewer
biology/py-dna-features-viewer: Add missing dependency
2022-02-12 09:12:39 -06:00
py-dnaio
…
py-ete3
devel/py-qt5, devel/py-sip: Update versions
2022-03-07 18:39:13 +01:00
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: Update 1.1.4 -> 1.1.5
2022-04-07 13:19:03 -07:00
py-libsedml
biology/{,py-}libsedml: Update 2.0.28 -> 2.0.30
2022-04-07 13:19:03 -07:00
py-loompy
biology/py-loompy: Update 3.0.6 -> 3.0.7
2022-03-06 09:09:59 -08:00
py-macs2
…
py-multiqc
…
py-ont-fast5-api
biology/py-ont-fast5-api: Update to 4.0.2
2022-03-25 11:37:29 -05:00
py-orange3-bioinformatics
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
2022-01-23 21:56:25 +01:00
py-orange3-single-cell
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
2022-01-23 21:56:25 +01:00
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: Update 0.16.0.1 -> 0.18.0
2021-12-19 23:48:52 -08:00
py-PySCeS
biology/py-PySCeS: fix with Python ≠ 3.8
2022-03-02 19:49:25 +01:00
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 13.8.0 -> 14.0.0
2022-01-19 10:10:01 -08:00
py-scikit-bio
biology/py-scikit-bio: build with clang on powerpc64le
2022-04-19 14:09:20 +02:00
py-xenaPython
…
pyfasta
…
python-nexus
biology/python-nexus: Fix build with setuptools 58.0.0+
2022-03-25 21:38:05 +08:00
rainbow
…
rampler
…
readseq
…
recombine
…
ruby-bio
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
rubygem-bio
biology/rubygem-bio: Update to 2.0.3
2022-01-12 02:47:28 +08:00
rubygem-bio-executables
…
rubygem-bio-old-biofetch-emulator
…
rubygem-bio-shell
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
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 1.15
2022-02-26 09:04:10 -06:00
scrm
…
seaview
biology/seaview: Update version 5.0.4=>5.0.5
2021-12-05 19:02:42 -06:00
seqan
*/*: Remove redundant '-[0-9]*' from CONFLICTS
2021-10-29 11:50:18 +02:00
seqan1
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
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 2.1.0 -> 2.2.0
2022-04-19 20:44:55 -07:00
seqtk
biology/seqtk: Update to 1.3
2021-12-18 13:37:06 -06:00
sigviewer
misc/: Update 0.99.6-2 -> 0.991
2021-08-18 10:17:45 -07:00
sim4
…
slclust
…
smithwaterman
…
snpeff
…
spoa
devel/cpu_features: Install cmake files, install headers into a dedicated directory
2022-01-26 08:45:29 -08:00
sra-tools
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
stacks
…
star
biology/star: Update to 2.7.9a
2021-11-26 15:57:02 -06:00
stringtie
…
subread
…
tabixpp
…
taxonkit
*/*: Bump PORTREVISION after lang/go 1.18 update
2022-03-30 03:01:44 -04:00
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
*/*: Bump PORTREVISION after lang/go 1.18 update
2022-03-30 03:01:44 -04:00
vcf2hap
biology/vcf2hap: Update to 0.1.5
2022-03-15 16:45:04 -05:00
vcf-split
biology/vcf-split: Update to 0.1.4
2022-03-15 16:43:40 -05:00
vcflib
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
vcftools
biology/vcftools: Add CPE information
2021-09-25 20:28:38 +00:00
velvet
…
viennarna
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
vsearch
biology/vsearch: Update to 2.21.1
2022-01-23 16:32:43 -06:00
vt
…
wise
…
Makefile
biology/fastq-trim: Lightening fast sequence read trimmer
2022-03-19 07:25:58 -05:00