mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2025-02-03 11:12:13 +00:00
Code Issues Releases Activity
freebsd-ports/biology
History
Yuri Victorovich dda16bd485 biology/checkm: Update 1.1.11 -> 1.2.0 
Reported by:	portscout
2022-05-01 11:14:09 -07:00
..
abyss
…
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
…
bamutil
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
bbmap
…
bcftools
biology/bcftools: Update to 1.15
2022-02-26 09:04:10 -06:00
bedtools
…
bfc
…
bio-mocha
biology/bio-mocha: Update bcftools submodule to 1.15
2022-02-26 09:04:10 -06:00
bioawk
…
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
…
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 CFLAGS_powerpc64
2022-04-21 17:11:13 +00:00
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: check for omp.h on all architectures
2022-04-27 13:22:07 +00:00
cdbfasta
…
checkm
biology/checkm: Update 1.1.11 -> 1.2.0
2022-05-01 11:14:09 -07:00
clustal-omega
…
clustalw
…
cufflinks
Fix CONFLICTS entries of multiple ports
2022-01-10 16:15:39 +01:00
cytoscape
…
ddocent
…
diamond
biology/diamond: Update to 2.0.15
2022-04-24 14:50:21 -03:00
dsr-pdb
biology/dsr-pdb: Remove -pg (mcount instrumentation) flag
2022-03-21 17:07:11 -07:00
edlib
…
emboss
…
erminej
…
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
…
fasttree
biology/fasttree: check for omp.h on all architectures
2022-04-27 13:22:02 +00:00
fastx-toolkit
Update CONFLICTS definitions in categories a* to c*
2022-02-06 19:36:07 +01:00
figtree
…
flash
…
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
…
hhsuite
biology/hhsuite: check for omp.h on all architectures
2022-04-27 13:22:04 +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: Update to 2.5.38
2022-04-24 15:24:30 -03:00
igv
…
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
…
jellyfish
…
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
…
libnuml
biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6
2022-04-23 18:36:56 -07:00
libsbml
textproc/libxml2: bump all LIB_DEPENDS consumers
2022-04-10 15:11:41 -04:00
libsedml
biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31
2022-04-22 11:04:38 -07:00
linux-foldingathome
…
mafft
…
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
…
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+: check for omp.h on all architectures
2022-04-27 13:22:09 +00:00
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
…
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
…
pbseqan
…
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: use openmp only when omp.h is present
2022-04-27 13:22:12 +00:00
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
…
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
…
py-deeptoolsintervals
…
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
…
py-gtfparse
…
py-hits
…
py-libnuml
biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6
2022-04-23 18:36:56 -07:00
py-libsedml
biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31
2022-04-22 11:04:38 -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-mrcfile
biology/py-mrcfile: New port: MRC file I/O library which is used in structural biology
2022-05-01 10:37:04 -07:00
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
…
py-pybigwig
…
py-pyfaidx
…
py-pysam
biology/py-pysam: Update 0.18.0 -> 0.19.0
2022-04-27 10:38:26 -07:00
py-PySCeS
biology/py-PySCeS: fix with Python ≠ 3.8
2022-03-02 19:49:25 +01:00
py-python-libsbml
…
py-pywgsim
…
py-resdk
biology/py-resdk: Update 14.0.0 -> 14.1.0
2022-04-27 10:38:25 -07:00
py-scikit-bio
biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64
2022-04-21 17:11:15 +00:00
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
…
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
…
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
biology/seqan-apps: remove obsolete USE_GCC
2022-04-25 14:12:52 +00:00
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
…
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
…
treepuzzle
…
trimadap
…
trimmomatic
…
tRNAscan-SE
…
ucsc-userapps
…
ugene
…
unikmer
biology/unikmer: Update 0.18.8 -> 0.19.0
2022-04-26 11:51:57 -07:00
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
…
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-mrcfile: New port: MRC file I/O library which is used in structural biology
2022-05-01 10:37:04 -07:00