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freebsd-ports/biology
History
Antoine Brodin 13b62c630f Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
..
ariadne
Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
artemis
…
avida
…
babel
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bamtools
biology/bamtools: API and toolkit for handling BAM files
2018-03-28 13:26:31 +00:00
bcftools
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bedtools
biology/bedtools: Upgrade to 2.27.1
2018-04-19 16:44:59 +00:00
biococoa
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blat
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bowtie
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
bowtie2
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bwa
Multiple ports:
2018-01-31 01:07:07 +00:00
canu
biology/canu: Upgrade to 1.7 release
2018-04-26 04:16:15 +00:00
cd-hit
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
cdbfasta
Multiple ports:
2018-01-31 01:07:07 +00:00
chemeq
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clustalw
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consed
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crux
Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
ddocent
biology/ddocent: Bash pipeline for RAD sequencing
2018-04-20 01:34:05 +00:00
diamond
biology/diamond: Update to version 0.9.21
2018-04-20 21:23:27 +00:00
emboss
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fasta
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fasta3
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fastahack
biology/fastahack: Utility for indexing and sequence extraction from FASTA files
2018-04-16 14:50:46 +00:00
fastdnaml
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fastool
Multiple ports:
2018-01-31 01:07:07 +00:00
fastqc
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fasttree
Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.
2018-03-18 13:38:23 +00:00
fastx-toolkit
Multiple ports:
2018-01-31 01:07:07 +00:00
fluctuate
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freebayes
biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping
2018-04-20 00:07:27 +00:00
garlic
Return maho@'s ports to the pool after his commit bit expired.
2018-03-11 11:20:43 +00:00
gff2ps
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gmap
Multiple ports:
2018-01-31 01:07:07 +00:00
gperiodic
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grappa
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hmmer
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htslib
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iolib
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iqtree
biology/iqtree: Update to version 1.6.4
2018-04-30 16:37:22 +00:00
jalview
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jellyfish
Multiple ports:
2018-01-31 01:07:07 +00:00
kallisto
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lagan
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lamarc
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libgtextutils
biology/libgtextutils: Unbreak for FreeBSD 12
2018-03-29 15:41:07 +00:00
libsbml
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linux-foldingathome
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mafft
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mapm3
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migrate
Mark broken on armvX and mips.
2018-03-18 13:48:07 +00:00
molden
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
mopac
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
mrbayes
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mummer
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muscle
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ncbi-blast+
biology/ncbi-blast+: Upgrade to 2.7.1
2018-03-27 18:04:21 +00:00
ncbi-toolkit
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njplot
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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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-FeatureIO
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p5-Bio-GFF3
…
p5-Bio-Glite
…
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-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
p5-TrimGalore
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paml
biology/paml: Set PORTVERSION directly
2018-04-26 15:36:30 +00:00
pbbam
biology/pbbam: PacBio BAM C++ library, with SWIG bindings
2018-04-23 16:08:21 +00:00
pbcopper
biology/pbcopper: Core C++ library for Pacific Biosciences tools
2018-04-23 16:23:53 +00:00
pbseqan
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
2018-04-21 17:21:30 +00:00
pear-merger
biology/pear-merger: Memory-efficient and accurate paired-end read merger
2018-04-04 17:21:39 +00:00
phrap
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phred
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phylip
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phyml
Remove now-useless, commented-out lines.
2018-03-10 23:35:03 +00:00
plink
Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
plinkseq
Multiple ports:
2018-01-31 01:07:07 +00:00
primer3
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protomol
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psi88
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-biom-format
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-biopython
- Update to 1.71
2018-04-09 06:26:18 +00:00
py-bx-python
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-cutadapt
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
2018-04-25 16:42:37 +00:00
py-macs2
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
py-pysam
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
2018-04-25 16:42:37 +00:00
pycogent
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
pyfasta
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
python-nexus
- Update to 1.61
2018-04-01 11:52:08 +00:00
rainbow
biology/rainbow: Efficient clustering and assembling of short reads
2018-04-02 16:50:46 +00:00
recombine
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ruby-bio
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rubygem-bio
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samtools
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seaview
biology/seaview: Update version 4.6.3=>4.6.5
2018-04-24 12:31:32 +00:00
seqan
biology/seqan-apps, biology/seqan: Update to 2.4.0
2018-03-10 06:21:37 +00:00
seqan1
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seqan-apps
devel/boost-*: update to 1.67.0
2018-04-18 13:57:42 +00:00
seqio
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seqtk
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
2018-04-03 20:57:05 +00:00
seqtools
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sim4
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slclust
Multiple ports:
2018-01-31 01:07:07 +00:00
smithwaterman
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
2018-04-15 17:45:52 +00:00
ssaha
Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
stacks
biology/stacks: Software pipeline for building loci from short-read sequences
2018-03-31 13:16:05 +00:00
t_coffee
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
tabixpp
biology/tabixpp: C++ wrapper to tabix indexer
2018-04-14 23:52:16 +00:00
tinker
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
treepuzzle
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trimadap
biology/trimadap: Trim adapter sequences from Illumina data
2018-04-03 18:23:54 +00:00
trimmomatic
Multiple ports:
2018-01-31 01:07:07 +00:00
tRNAscan-SE
Deprecate ports broken for more than 6 months
2018-05-05 10:49:36 +00:00
ugene
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unanimity
biology/unanimity: Pacific Biosciences consensus library and applications
2018-04-24 14:16:46 +00:00
vcflib
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files
2018-04-17 03:11:39 +00:00
vcftools
Multiple ports:
2018-01-31 01:07:07 +00:00
velvet
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wise
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xmolwt
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Makefile
biology/unanimity: Pacific Biosciences consensus library and applications
2018-04-24 14:16:46 +00:00