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freebsd-ports/biology
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Joseph Mingrone 9c4faf08b0 biology/hyphy: Update to version 2.5.17 
Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.16
https://github.com/veg/hyphy/releases/tag/2.5.17
2020-08-20 16:15:22 +00:00
..
abyss
Chanse update of devel/libffi
2020-07-04 18:11:42 +00:00
artemis
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avida
…
babel
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bamtools
Bump devel/jsoncpp consumers after r540853.
2020-06-30 17:46:18 +00:00
bcftools
biology/bcftools: Upgrade to 1.10.2
2020-08-03 18:16:54 +00:00
bedtools
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bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
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bolt-lmm
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
2020-05-06 16:11:14 +00:00
bowtie
biology/bowtie: Unbreak build with GCC 10
2020-07-04 10:46:08 +00:00
bowtie2
Update devel/tbb to 2020.3 and bump dependent ports' revisions
2020-07-17 10:12:25 +00:00
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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
cytoscape
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ddocent
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diamond
biology/diamond: Update to version 2.0.2
2020-08-07 11:20:11 +00:00
dsr-pdb
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emboss
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
exonerate
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fasta
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fasta3
…
fastahack
…
fastdnaml
…
fastool
…
fastp
…
fastqc
…
fasttree
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fastx-toolkit
…
figtree
…
fluctuate
…
freebayes
…
garlic
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gatk
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
2020-07-09 00:40:56 +00:00
gcta
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
2020-05-06 16:11:14 +00:00
gemma
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
2020-05-06 16:39:12 +00:00
gff2ps
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gmap
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gperiodic
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graphlan
biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
2020-08-14 04:59:29 +00:00
grappa
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groopm
biology/groopm: Remove python's 2.7 restriction placed here by mistake
2020-08-13 19:19:23 +00:00
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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
hyphy
biology/hyphy: Update to version 2.5.17
2020-08-20 16:15:22 +00:00
igv
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infernal
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iolib
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iqtree
biology/iqtree: Update to version 2.0.6
2020-05-30 18:43:26 +00:00
jalview
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jellyfish
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
kallisto
biology/kallisto: Revert to 0.46.1
2020-08-03 15:45:21 +00:00
lagan
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lamarc
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libbigwig
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libgtextutils
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libsbml
Move devel/swig30 to devel/swig and update to 4.0.1
2020-06-17 18:17:45 +00:00
linux-foldingathome
Update to 7.6.13
2020-05-09 13:21:29 +00:00
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
Update devel/gmake to 4.3.
2020-05-09 19:24:49 +00:00
mrbayes
- Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:47:57 +00:00
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
…
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
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
2020-06-26 11:55:23 +00:00
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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
pbcopper
Deprecate ports broken for more than 6 months
2020-07-26 07:32:00 +00:00
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
biology/phyml: update to 3.3.20200621
2020-07-10 09:45:48 +00:00
picard-tools
biology/picard-tools: CLI tools for manipulating sequencing data
2020-06-13 13:54:47 +00:00
plink
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
2020-05-06 16:39:12 +00:00
primer3
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prodigal
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prodigy-lig
Unbreak bulk -a
2020-06-13 15:05:44 +00:00
protomol
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psi88
biology/psi88: Unbreak build with GCC 10
2020-07-04 12:15:58 +00:00
py-biopython
biology/py-biopython: Set python requirement to 3.6+
2020-06-13 13:42:12 +00:00
py-bx-python
biology/py-bx-python: Update 0.8.8 -> 0.8.9
2020-06-26 04:17:11 +00:00
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
Unbreak bulk -a
2020-07-14 07:59:28 +00:00
py-gtfparse
biology/py-gtfparse: Update 1.2.0 -> 1.2.1
2020-08-07 04:13:00 +00:00
py-hits
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
2020-05-16 03:11:05 +00:00
py-loompy
biology/py-loompy: Update 2.0.17 -> 3.0.6
2020-06-16 02:26:08 +00:00
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
Clean up some things
2020-05-30 00:57:02 +00:00
py-pyfaidx
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py-pysam
biology/py-pysam: Update 0.15.4 -> 0.16.0
2020-06-09 05:03:48 +00:00
py-scikit-bio
devel/ipython: Update to 7.17.0
2020-08-15 12:50:57 +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
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
2020-05-05 14:22:09 +00:00
rubygem-bio
Update to 2.0.1
2020-07-24 07:49:43 +00:00
rubygem-bio-executables
Add rubygem-bio-executables 1.0.0
2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator
Add rubygem-bio-old-biofetch-emulator 1.0.0
2020-07-24 07:08:05 +00:00
rubygem-bio-shell
Add rubygem-bio-shell 1.0.0
2020-07-24 07:08:11 +00:00
samtools
biology/samtools: Upgrade to 1.10
2020-08-03 18:22:06 +00:00
scrm
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
2020-05-15 07:30:34 +00:00
seaview
biology/seaview: Update version 5.0.3=>5.0.4
2020-06-22 17:34:44 +00:00
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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subread
biology/subread: Read alignment, quantification and mutation discovery
2020-06-05 01:55:49 +00:00
tabixpp
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
vcftools
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velvet
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viennarna
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
vsearch
biology/vsearch: Update to 2.15.0
2020-06-20 14:31:59 +00:00
vt
biology/vt: Patch to work with htslib 1.10.2
2020-08-03 17:42:32 +00:00
wise
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Makefile
Remove deprecated ports:
2020-08-15 10:50:58 +00:00