freebsd-ports/biology
2022-08-13 20:54:30 +02:00
..
abyss devel/libffi: Bump deps PORTREVISION for shlib change 2022-05-09 12:23:51 -07:00
ad2vcf biology/ad2vcf: Update to 0.1.6 2022-06-11 09:26:57 -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
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 0.2.3 2022-06-11 09:26:56 -05:00
biolibc-tools *: bump PORTREVISION of devel/xxhash users. 2022-08-13 20:54:30 +02:00
bioparser
biosig biology/biosig: Update 2.4.1 -> 2.4.2 2022-06-19 09:53:42 -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 devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
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 devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
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 biology/cufflinks: Unbreak 2022-07-27 20:43:46 -07:00
cytoscape
ddocent
diamond biology/diamond: Update to 2.0.15 2022-04-24 14:50:21 -03:00
dsr-pdb devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
edlib
emboss */*: Remove redundant '-[0-9]*' from CONFLICTS 2021-10-29 11:50:18 +02:00
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: Use Java 17 instead of EOLed Java 12 2022-05-24 15:39:38 -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 devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
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 2.5.39 2022-05-26 23:38:12 -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 devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
jalview
jellyfish
kallisto */*: Replace science/szip with science/libaec 2022-06-16 23:13:01 +08:00
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 2.0.31 -> 2.0.32 2022-06-08 22:53:28 -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 biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled 2022-07-23 09:41:44 -07:00
molden biology/molden: Unbreak build; Correct WWW 2022-07-19 01:07:49 -07:00
mothur biology/mothur: Update 1.47.0 -> 1.48.0 2022-05-19 19:10:18 -07:00
mrbayes
mummer Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
muscle
ncbi-blast+ devel/grpc: Update to 1.47.0 2022-06-30 00:32:34 +08:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Broken on armv6 2022-08-06 16:29:45 -07:00
ncbi-entrez-direct */*: Bump port revisons after lang/go{117,118} update 2022-06-07 16:56:10 -05:00
ncbi-toolkit Fix CONFLICTS_INSTALL in benchmarks and biology 2022-06-29 16:53:54 +02:00
ncbi-vdb textproc/libxml2: bump all LIB_DEPENDS consumers 2022-04-10 15:11:41 -04:00
ngs-sdk biology/ngs-sdk: Broken on armv6, armv7 2022-07-22 15:35:02 -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 devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
pbseqan
peak-classifier biology/peak-classifier: Update to 0.1.4 2022-06-11 09:26:57 -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: Update to 3.1.1 2022-05-08 07:48:38 -05:00
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 biology/py-gffutils: Update 0.10.1 -> 0.11.0 2022-06-06 17:38:48 -07:00
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 2.0.31 -> 2.0.32 2022-06-08 22:53:28 -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: Remove BROKEN lines 2022-07-19 08:53:29 -07:00
py-PySCeS biology/py-PySCeS: Update 1.0.1 -> 1.0.2 2022-05-20 15:02:59 -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
py-resdk biology/py-resdk: Update 14.1.0 -> 15.0.0 2022-06-06 17:38:49 -07:00
py-scikit-bio biology/py-scikit-bio: Broken on aarch64 2022-06-03 15:56:03 -07:00
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 */*: 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 3.1.0 -> 3.2.0 2022-06-24 00:20:46 -07:00
seqan-apps devel/cmake: Update to 3.23.0 2022-05-16 08:49:43 +02:00
seqio
seqkit */*: Bump port revisons after lang/go{117,118} update 2022-06-07 16:56:10 -05:00
seqtk biology/seqtk: Update to 1.3 2021-12-18 13:37:06 -06:00
sigviewer
sim4
slclust
smithwaterman
snpeff cleanup: remove expired versions of OpenJDK (12 through 16) 2022-05-24 22:09:35 +02:00
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: Broken on systems where OpenMP isn't enabled 2022-07-23 18:25:22 -07:00
stringtie
subread
tabixpp
taxonkit biology/taxonkit: Update 0.11.1 -> 0.12.0 2022-06-08 23:08:00 -07:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene biology/ugene: Correct BROKEN message 2022-08-04 09:36:57 -07:00
unikmer */*: Bump port revisons after lang/go{117,118} update 2022-06-07 16:56:10 -05:00
vcf2hap biology/vcf2hap: Update to 0.1.6 2022-06-11 09:26:57 -05:00
vcf-split biology/vcf-split: Update to 0.1.5 2022-06-11 09:26:56 -05:00
vcflib Fix CONFLICTS_INSTALL in benchmarks and biology 2022-06-29 16:53:54 +02:00
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/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take maintainership 2022-06-19 00:52:28 -07:00