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freebsd-ports/biology
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Jason W. Bacon 176e391e4b biology/py-biopython: Upgrade to 1.77 
Upstream support for python 3

PR:             ports/246763
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
2020-05-29 02:03:29 +00:00
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abyss
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artemis
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avida
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babel
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bamtools
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bcftools
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bedtools
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biococoa
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bolt-lmm
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bowtie
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bowtie2
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bwa
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canu
Mark as BROKEN on powerpc64:
2020-05-17 02:25:16 +00:00
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
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dsr-pdb
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emboss
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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
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fastqc
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fasttree
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fastx-toolkit
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figtree
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fluctuate
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freebayes
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garlic
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gatk
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
2020-05-28 02:26:51 +00:00
gcta
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gemma
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gff2ps
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gmap
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gperiodic
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graphlan
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grappa
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groopm
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haplohseq
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hhsuite
biology/hhsuite: fix build on powerpc64 elfv2
2020-05-11 19:33:32 +00:00
hisat2
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hmmer
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htslib
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hyphy
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igv
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infernal
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iolib
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iqtree
biology/iqtree: Update to version 2.0.5
2020-05-28 00:27:13 +00:00
jalview
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jellyfish
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kallisto
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lagan
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lamarc
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libbigwig
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libgtextutils
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libsbml
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linux-foldingathome
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mafft
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mapm3
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migrate
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minimap2
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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+
Bump PORTREVISION for security/nettle shlib change
2020-05-16 10:51:32 +00:00
ncbi-cxx-toolkit
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ncbi-toolkit
Bump PORTREVISION for security/nettle shlib change
2020-05-16 10:51:32 +00:00
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
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pbcopper
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pbseqan
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pear-merger
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phrap
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
2020-05-27 11:59:13 +00:00
phred
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phylip
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phyml
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plink
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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: Upgrade to 1.77
2020-05-29 02:03:29 +00:00
py-bx-python
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py-cutadapt
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py-dnaio
biology/py-dnaio: Upgrade to 0.4.2
2020-05-24 15:23:15 +00:00
py-ete3
New port: biology/py-ete3: Framework for the analysis and visualization of trees
2020-05-16 00:13:09 +00:00
py-fastTSNE
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py-Genesis-PyAPI
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py-gffutils
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py-gtfparse
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py-hits
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
2020-05-16 03:11:05 +00:00
py-loompy
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py-macs2
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py-multiqc
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py-orange3-bioinformatics
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py-orange3-single-cell
Update Sphinx
2020-05-11 23:51:58 +00:00
py-pandas-charm
New port: biology/py-pandas-charm: Library for getting character matrices into and out of pandas
2020-05-16 00:14:16 +00:00
py-pyfaidx
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py-pysam
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py-scikit-bio
biology/py-scikit-bio: Fix license
2020-05-16 02:29:20 +00:00
py-xenaPython
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pyfasta
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python-nexus
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rainbow
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recombine
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ruby-bio
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rubygem-bio
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samtools
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scrm
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
2020-05-15 07:30:34 +00:00
seaview
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seqan
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seqan1
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seqan-apps
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seqio
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seqtk
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sim4
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slclust
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smithwaterman
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stacks
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star
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stringtie
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tabixpp
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tophat
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treekin
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treepuzzle
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trimadap
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trimmomatic
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tRNAscan-SE
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ugene
biology/ugene: prepare for Qt5-5.15
2020-05-19 18:00:02 +00:00
vcflib
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vcftools
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velvet
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viennarna
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vsearch
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wise
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Makefile
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
2020-05-16 03:11:05 +00:00