mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2025-02-05 11:35:01 +00:00
Code Issues Releases Activity
freebsd-ports/biology
History
Yuri Victorovich 9b5fb66610 biology/{,py-}libsedml: Update 2.0.26 -> 2.0.27
2022-02-16 16:27:20 -08:00
..
abyss
cleanup: drop support for EOL FreeBSD 11.X
2021-09-30 23:23:30 +02:00
ad2vcf
biology/ad2vcf: Update to 0.1.4
2021-12-14 13:45:31 -06:00
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
math/gsl: bump portrevision of consumers after update to 2.7.1
2022-01-12 20:41:22 +01:00
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 to 1.14-20220112
2022-01-13 13:00:41 -06:00
bioawk
…
biococoa
…
biolibc
biology/biolibc: Update to 0.2.1
2021-12-14 13:45:31 -06:00
biolibc-tools
biology/biolibc-tools: Update to 0.1.1
2021-12-14 13:45:32 -06:00
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: Allow package build on non-amd64 systems
2021-12-01 09:49:28 -06:00
bolt-lmm
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
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
…
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
…
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
fastqc
…
fasttree
…
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
…
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
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
gmap
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
gperiodic
…
graphlan
…
groopm
…
haplohseq
…
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 1.14
2021-12-18 11:56:50 -06:00
hyphy
biology/hyphy: Update to 2.5.36
2022-02-03 01:42:15 -04:00
igv
cleanup: drop support for EOL FreeBSD 11.X
2021-09-30 23:23:30 +02:00
infernal
…
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
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/{,py-}libsedml: Update 2.0.26 -> 2.0.27
2022-02-16 16:27:20 -08:00
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+
biology/ncbi-blast+: fix build on powerpc
2022-01-22 13:33:19 +00:00
ncbi-cxx-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
ncbi-entrez-direct
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
ncbi-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
ncbi-vdb
security/mbedtls: Update to 2.28.0 and fix make test
2022-01-28 13:14:09 +01:00
ngs-sdk
biology/ngs-sdk: Update 2.11.1 -> 2.11.2
2022-01-27 01:29:09 -08:00
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 0.1.2
2021-12-14 13:45:32 -06:00
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 1.82
2022-02-10 15:23:48 +01:00
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: chase ad5a0604c41c
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-dna-features-viewer
biology/py-dna-features-viewer: Add missing dependency
2022-02-12 09:12:39 -06:00
py-dnaio
…
py-ete3
PyQt: Update sip to 6.5.0, reintroduce sip4 and simplify PyQt framework.
2022-01-27 07:12:26 +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: fix install with python 3.10+
2021-11-02 21:08:32 +03:00
py-libsedml
biology/{,py-}libsedml: Update 2.0.26 -> 2.0.27
2022-02-16 16:27:20 -08:00
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
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: 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 13.8.0 -> 14.0.0
2022-01-19 10:10:01 -08:00
py-scikit-bio
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
py-xenaPython
…
pyfasta
…
python-nexus
…
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 1.14
2021-12-18 11:56:51 -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 2.0.1 -> 2.1.0
2021-11-16 10:57:47 -08:00
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
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
stacks
…
star
biology/star: Update to 2.7.9a
2021-11-26 15:57:02 -06:00
stringtie
…
subread
…
tabixpp
…
taxonkit
biology/taxonkit: Update 0.8.0 -> 0.9.0
2021-12-02 12:57:06 -08:00
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
biology/unikmer: Update 0.18.4 -> 0.18.8
2021-09-26 01:54:07 -07:00
vcf2hap
biology/vcf2hap: Update to 0.1.4
2021-12-14 13:45:32 -06:00
vcf-split
biology/vcf-split: Update to 0.1.3.3
2021-12-14 13:45:32 -06:00
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/py-bcbio-gff: Read and write Generic Feature Format (GFF)
2022-02-03 13:38:42 -06:00