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freebsd-ports/biology
History
Piotr Kubaj 123f5e1c0c biology/hyphy: enable on powerpc and powerpc64
2021-11-07 12:14:59 +00:00
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abyss
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ad2vcf
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artemis
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avida
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babel
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bamtools
devel/jsoncpp: Update to 1.9.4 -> 1.9.5
2021-11-05 12:09:19 -07:00
bamutil
biology/bamutil: Update to 1.0.15
2021-10-20 14:43:38 -05:00
bbmap
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bcftools
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bedtools
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bfc
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bioawk
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biococoa
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biolibc
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biolibc-tools
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bioparser
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biosig
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biosoup
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biostar-tools
biology/biostar-tools: Add biology/igv to metaport deps
2021-10-30 10:27:03 -05:00
bolt-lmm
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bowtie
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bowtie2
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bwa
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canu
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cd-hit
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cdbfasta
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checkm
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clustal-omega
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clustalw
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cufflinks
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cytoscape
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ddocent
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diamond
biology/diamond: Update to 2.0.12
2021-10-12 12:40:55 -03:00
dsr-pdb
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edlib
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emboss
*/*: Remove redundant '-[0-9]*' from CONFLICTS
2021-10-29 11:50:18 +02:00
erminej
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exonerate
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fasta
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fasta3
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fastahack
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fastdnaml
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fastool
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fastp
biology/fastp: Update to 0.23.1
2021-10-20 11:37:39 -05:00
fastqc
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fasttree
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fastx-toolkit
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figtree
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flash
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fluctuate
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freebayes
biology/freebayes: builds fine on armv7
2021-11-05 01:14:22 +00:00
garlic
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gatk
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gcta
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gemma
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generand
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gff2ps
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gmap
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
2021-10-25 12:58:29 +00:00
gperiodic
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graphlan
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groopm
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haplohseq
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hhsuite
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hisat2
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hmmer
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htslib
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hyphy
biology/hyphy: enable on powerpc and powerpc64
2021-11-07 12:14:59 +00:00
igv
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infernal
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iolib
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iqtree
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jalview
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jellyfish
*: Clean up some things
2021-10-12 17:01:38 +02:00
kallisto
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lamarc
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libbigwig
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libgtextutils
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libneurosim
biology/libneurosim: New port: Common interfaces for neuronal simulators
2021-10-08 10:20:27 -07:00
libnuml
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libsbml
biology/libsbml: Fix build with Python 3.10
2021-11-02 05:28:40 +08:00
libsedml
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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
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migrate
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minimap2
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
2021-10-25 12:58:29 +00:00
mmseqs2
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molden
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mopac
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mothur
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mrbayes
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mummer
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muscle
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ncbi-blast+
devel/grpc: Update to 1.41.0
2021-10-25 23:57:13 +08:00
ncbi-cxx-toolkit
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ncbi-entrez-direct
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ncbi-toolkit
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ncbi-vdb
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ngs-sdk
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
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p5-TrimGalore
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paml
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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
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pear-merger
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phrap
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phred
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phyml
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picard-tools
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plink
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pooler
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primer3
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prodigal
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prodigy-lig
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protomol
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psi88
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py-biom-format
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py-biopython
biology/py-biopython: Update to 1.79
2021-10-12 14:43:04 +08:00
py-bx-python
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py-crossmap
biology/py-crossmap: chase ad5a0604c41c
2021-10-14 00:53:16 +00:00
py-cutadapt
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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-dnaio
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py-ete3
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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py-gtfparse
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py-hits
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py-libnuml
biology/py-libnuml: fix install with python 3.10+
2021-11-02 21:08:32 +03:00
py-libsedml
biology/py-libsedml: fix install with python 3.10+
2021-11-02 21:08:31 +03:00
py-loompy
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py-macs2
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py-multiqc
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py-ont-fast5-api
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py-orange3-bioinformatics
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py-orange3-single-cell
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py-pandas-charm
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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
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py-pysam
biology/py-pysam: limit supported python versions
2021-11-01 16:59:09 +03:00
py-PySCeS
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py-python-libsbml
biology/py-python-libsbml: limit supported python versions, fix build
2021-11-03 21:26:41 +03:00
py-pywgsim
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py-resdk
biology/py-resdk: Update 13.4.0 -> 13.6.0
2021-10-22 01:57:04 -07:00
py-scikit-bio
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py-xenaPython
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pyfasta
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python-nexus
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rainbow
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rampler
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readseq
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recombine
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ruby-bio
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rubygem-bio
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rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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sam2pairwise
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samtools
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scrm
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seaview
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seqan
*/*: Remove redundant '-[0-9]*' from CONFLICTS
2021-10-29 11:50:18 +02:00
seqan1
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seqan3
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seqan-apps
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seqio
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seqkit
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seqtk
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sigviewer
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sim4
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slclust
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smithwaterman
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snpeff
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spoa
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sra-tools
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stacks
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star
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stringtie
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subread
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tabixpp
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taxonkit
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treekin
biology/treekin: Unbreak
2021-10-15 08:50:24 -07:00
treepuzzle
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trimadap
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
2021-10-25 12:58:29 +00:00
trimmomatic
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tRNAscan-SE
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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
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vcf2hap
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vcf-split
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vcflib
biology/vcflib: Update to 1.0.2
2021-11-04 09:23:17 -05:00
vcftools
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velvet
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viennarna
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vsearch
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
2021-10-25 12:58:29 +00:00
vt
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wise
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Makefile
*/Makefile: Sort SUBDIRs
2021-10-25 23:57:04 +08:00