freebsd-ports/biology
2022-08-04 09:21:46 -07:00
..
abyss biology/abyss: Add test target 2022-07-30 00:34:34 -07:00
ad2vcf biology/ad2vcf: Update to 0.1.6 2022-06-11 09:26:57 -05:00
artemis biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
avida biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
babel biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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
biococoa
biolibc biology/biolibc: Update to 0.2.3 2022-06-11 09:26:56 -05:00
biolibc-tools biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
bioparser biology/bioparser: Update 3.0.12-2 -> 3.0.15 2021-09-21 09:41:49 -07:00
biosig biology/biosig: Update 2.4.1 -> 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: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
checkm biology/checkm: Update 1.1.11 -> 1.2.0 2022-05-01 11:14:09 -07:00
clustal-omega
clustalw biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
cufflinks biology/cufflinks: Unbreak 2022-07-27 20:43:06 -07:00
cytoscape biology/cytoscape: mark unconditionally BROKEN 2021-05-12 14:55:52 +03:00
ddocent cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
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 biology/edlib: Update 1.2.6.20201202 -> 1.2.7 2021-08-21 10:12:15 -07:00
emboss biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
erminej biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00
exonerate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fasta biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fasta3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
fastahack
fastdnaml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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 biology/flash: Fast Length Adjustment of SHort reads 2021-08-23 12:26:47 -05:00
fluctuate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
freebayes biology/freebayes: Update to 1.3.6 2022-02-06 14:23:45 -06:00
garlic biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gatk biology/gatk: Use Java 17 instead of EOLed Java 12 2022-05-24 15:39:38 -07:00
gcta biology/gcta: Use bundled version of eigen3 2022-07-06 13:40:04 -07:00
gemma math/gsl: bump portrevision of consumers after update to 2.7.1 2022-01-12 20:41:22 +01:00
generand
gff2ps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gffread biology/gffread: remove local poudriere files 2022-03-07 23:44:38 +01:00
gmap biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
gperiodic cleanup: remove '$MCom' tag 2022-07-20 21:44:12 +02:00
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: Fix build on some architectures 2022-08-04 09:21:45 -07:00
hisat2 biology/hisat2: enable on riscv64 2021-12-16 22:38:56 +01:00
hmmer biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
htslib biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
hyphy biology/hyphy: Correct BROKEN message 2022-08-04 09:21:46 -07:00
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 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
iqtree devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
jalview biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
jellyfish *: Clean up some things 2021-10-12 17:01:38 +02:00
kallisto science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
lamarc biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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/{,py-}libnuml: Update 1.1.5 -> 1.1.6 2022-04-23 18:36:56 -07:00
libsbml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
libsedml biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32 2022-06-08 22:53:28 -07:00
linux-foldingathome biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mafft biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mapm3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
migrate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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 09:40:43 -07:00
molden biology/molden: Update 6.7 -> 7.1 2022-07-23 13:00:53 -07:00
mothur biology/mothur: Update 1.47.0 -> 1.48.0 2022-05-19 19:10:18 -07:00
mrbayes biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
mummer biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
muscle biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ncbi-blast+ devel/grpc: Update to 1.48.0 2022-07-30 13:57:09 +08:00
ncbi-cxx-toolkit Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
ncbi-entrez-direct all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
ncbi-toolkit biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ncbi-vdb science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
ngs-sdk biology/ngs-sdk: Broken on armv6, armv7 2022-07-22 15:34:07 -07:00
p5-AcePerl biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-ASN1-EntrezGene biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Cluster biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Coordinate biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Das biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Das-Lite biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-DB-EMBL biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-DB-NCBIHelper biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-FeatureIO biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-GFF3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Glite biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Graphics biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-MAGETAB biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-NEXUS biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Phylo biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-SCF biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-Bio-Variation biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-BioPerl biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-BioPerl-Run biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
p5-transdecoder
p5-TrimGalore
paml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
pbbam devel/boost-all: bump all library consumers after boost upgrade 2022-05-22 23:17:16 +03:00
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 0.1.4 2022-06-11 09:26:57 -05:00
pear-merger
phrap
phred biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
phyml biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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 1.85 2022-07-12 07:47:45 -05:00
primer3 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
prodigal
prodigy-lig
protomol biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
psi88 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
py-bx-python biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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: 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 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 1.1.5 -> 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: Update 1.4.0 -> 1.4.2 2022-07-29 01:46:46 -07:00
py-multiqc math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
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: Remove BROKEN lines 2022-07-19 08:51:56 -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 biology/py-pywgsim: Modified wgsim genomic data simulator 2021-09-06 07:55:49 -05:00
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 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
python-nexus biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rainbow
rampler
readseq
recombine biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ruby-bio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-executables biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-old-biofetch-emulator biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
rubygem-bio-shell biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
sam2pairwise biology/sam2pairwise: Show pairwise alignment for each read in a SAM file 2021-09-07 15:32:29 -05:00
samtools biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
scrm
seaview biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan-apps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan1 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqan3 biology/seqan3: Update 3.1.0 -> 3.2.0 2022-06-24 00:20:46 -07:00
seqio biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
seqkit all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
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 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
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 science/hdf5: bump PORTREVISION of consumers 2022-07-20 16:35:24 +02:00
stacks
star biology/star: Broken on systems where OpenMP isn't enabled 2022-07-23 18:24:10 -07:00
stringtie
subread
tabixpp
taxonkit all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
treekin biology/treekin: Unbreak 2021-10-15 08:50:24 -07:00
treepuzzle biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
trimadap Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
trimmomatic biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
tRNAscan-SE biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ucsc-userapps biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
ugene biology/ugene: Broken on systems where OpenMP isn't enabled 2022-08-04 00:41:24 -07:00
unikmer all: Bump PORTREVISION after Go update 2022-08-03 16:35:13 -05:00
vcf-split biology/vcf-split: Update to 0.1.5 2022-06-11 09:26:56 -05:00
vcf2hap biology/vcf2hap: Update to 0.1.6 2022-06-11 09:26:57 -05:00
vcflib Fix CONFLICTS_INSTALL in benchmarks and biology 2022-06-29 16:53:54 +02:00
vcftools biology/vcftools: Add CPE information 2021-09-25 20:28:38 +00:00
velvet biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
viennarna biology/viennarna: Update 2.5.0 -> 2.5.1 2022-07-31 01:12:49 -07:00
vsearch biology/vsearch: Update to 2.21.1 2022-01-23 16:32:43 -06:00
vt
wise biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
Makefile biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools 2022-07-06 18:33:58 -07:00