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Code Issues Releases Activity
freebsd-ports/biology
History
Yuri Victorovich d5c0a71815 biology/checkm: Update 1.0.13 -> 1.0.16 
Reported by:	portscout
2019-08-09 07:22:48 +00:00
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abyss
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
artemis
…
avida
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
babel
…
bamtools
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
bcftools
…
bedtools
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
biococoa
Move Objective-C ports to the v2 GNUstep ABI.
2019-02-03 15:37:58 +00:00
bolt-lmm
PR: 239613
2019-08-04 23:48:22 +00:00
bowtie
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
bowtie2
biology/bowtie2: Clarify CPU-specificity
2019-04-24 17:41:27 +00:00
bwa
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canu
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
cd-hit
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
cdbfasta
…
checkm
biology/checkm: Update 1.0.13 -> 1.0.16
2019-08-09 07:22:48 +00:00
chemeq
Mark BROKEN: unfetchable
2019-08-04 08:31:22 +00:00
clustal-omega
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clustalw
…
consed
…
cufflinks
biology/cufflinks: Fix build on i386 by removing the hard-coded -m64
2019-05-29 07:02:28 +00:00
cytoscape
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ddocent
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
diamond
biology/diamond: Update to version 0.9.25
2019-08-04 23:35:15 +00:00
dsr-pdb
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
emboss
…
exonerate
…
fasta
…
fasta3
…
fastahack
…
fastdnaml
…
fastool
…
fastp
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
fastqc
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fasttree
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
fastx-toolkit
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figtree
New port: biology/figtree: Graphical viewer of phylogenetic trees
2019-02-03 21:14:38 +00:00
fluctuate
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freebayes
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
garlic
…
gatk
biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43
2019-07-26 18:03:08 +00:00
gemma
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
gff2ps
biology/gff2ps: update 0.98d to 0.98l
2018-12-19 17:34:29 +00:00
gmap
Enable workaround for building on powerpc64.
2019-06-21 11:15:08 +00:00
gperiodic
Mark BROKEN: unfetchable
2019-08-04 08:31:22 +00:00
graphlan
New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
2019-02-03 20:13:26 +00:00
grappa
…
groopm
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
hhsuite
biology/hhsuite: fix build on powerpc64
2019-08-05 14:23:23 +00:00
hisat2
New port: biology/hisat2: Program for mapping next-generation sequencing reads
2019-01-11 16:02:05 +00:00
hmmer
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
htslib
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hyphy
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
igv
biology/igv: Update 2.5.2 -> 2.5.3
2019-06-01 20:49:20 +00:00
infernal
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iolib
- Fix build in head i386
2019-04-01 19:33:15 +00:00
iqtree
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
jalview
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jellyfish
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
kallisto
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
lagan
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lamarc
…
libbigwig
New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)
2019-07-11 17:05:22 +00:00
libgtextutils
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libsbml
Use USES=pathfix
2019-06-22 21:48:14 +00:00
linux-foldingathome
Mark BROKEN: unfetchable
2019-08-04 08:31:22 +00:00
mafft
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mapm3
…
migrate
…
minimap2
biology/minimap2: Upgrade to 2.17
2019-05-05 14:56:07 +00:00
molden
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
mopac
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
mothur
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
mrbayes
Update devel/readline to 8.0
2019-04-09 14:04:49 +00:00
mummer
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
muscle
…
ncbi-blast+
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
ncbi-cxx-toolkit
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
ncbi-toolkit
Update security/nettle to 3.5.1
2019-07-09 17:13:07 +00:00
ngs-sdk
Mark this port as not buildable on powerpc64:
2019-06-25 12:17:04 +00:00
p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
Add p5-Bio-Cluster 1.7.3
2019-02-20 20:46:37 +00:00
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
…
p5-Bio-GFF3
…
p5-Bio-Glite
…
p5-Bio-Graphics
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p5-Bio-MAGETAB
Fix typo
2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
- Add LICENSE
2019-03-30 09:01:08 +00:00
p5-BioPerl
Update to 1.007005 (1.7.5)
2019-02-22 19:54:12 +00:00
p5-BioPerl-Run
Update to 1.007003
2019-02-20 20:46:58 +00:00
p5-transdecoder
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
p5-TrimGalore
biology/p5-TrimGalore: Upgrade to 0.6.1
2019-03-24 21:44:17 +00:00
paml
biology/paml: Update to version 4.9i
2019-02-26 15:12:42 +00:00
pbbam
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
pbcopper
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
pbseqan
biology/pbseqan: Mark deprecated
2019-02-20 01:53:35 +00:00
pear-merger
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phrap
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phred
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phylip
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phyml
- Update to 3.3.20190321
2019-05-20 09:17:29 +00:00
plinkseq
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primer3
…
prodigal
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
2019-02-03 18:08:14 +00:00
prodigy-lig
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
protomol
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psi88
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-biom-format
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-biopython
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-bx-python
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-cutadapt
biology/py-cutadapt: Upgrade to 2.3
2019-04-27 01:26:17 +00:00
py-dnaio
biology/py-dnaio: Read and write FASTQ and FASTA
2019-03-24 19:40:26 +00:00
py-fastTSNE
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-Genesis-PyAPI
…
py-gffutils
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-gtfparse
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-loompy
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-macs2
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-orange3-bioinformatics
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-orange3-single-cell
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
py-pyfaidx
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-pysam
biology/py-pysam: Update 0.15.1 -> 0.15.2
2019-01-26 04:15:54 +00:00
py-xenaPython
New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub
2019-04-12 17:01:10 +00:00
pycogent
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
pyfasta
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
python-nexus
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rainbow
…
recombine
…
ruby-bio
…
rubygem-bio
…
samtools
…
seaview
…
seqan
…
seqan1
…
seqan-apps
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
seqio
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seqtk
…
seqtools
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
sim4
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slclust
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smithwaterman
…
stacks
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
star
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
stringtie
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t_coffee
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
tabixpp
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treekin
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
treepuzzle
…
trimadap
biology/trimadap: Mark only for amd64 and i386
2019-05-11 00:18:24 +00:00
trimmomatic
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tRNAscan-SE
biology/tRNAscan-SE: Update to 2.0.3
2019-06-08 01:31:18 +00:00
ugene
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +00:00
unanimity
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
vcflib
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vcftools
…
velvet
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viennarna
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
vsearch
biology/vsearch: Update to 2.13.4
2019-05-11 13:42:33 +00:00
wise
…
Makefile
New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)
2019-07-11 17:05:22 +00:00