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freebsd-ports/biology
History
Yuri Victorovich 74ca3eaba7 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
..
abyss
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +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
biology/bedtools: unbreak with libc++ 8
2019-03-04 06:55:08 +00:00
biococoa
Move Objective-C ports to the v2 GNUstep ABI.
2019-02-03 15:37:58 +00:00
bowtie
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
bowtie2
Mark as broken on aarch64:
2019-03-29 22:13:11 +00:00
bwa
…
canu
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
cd-hit
biology/cd-hit: Upgrade to 4.8.1
2019-03-14 23:59:47 +00:00
cdbfasta
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checkm
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
chemeq
…
clustal-omega
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clustalw
…
consed
…
cytoscape
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ddocent
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
diamond
biology/diamond: Update to version 0.9.24
2018-12-31 19:00:00 +00:00
dsr-pdb
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
emboss
…
exonerate
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fasta
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fasta3
…
fastahack
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fastdnaml
…
fastool
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fastqc
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fasttree
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +00:00
garlic
…
gatk
devel/gradle: Update to 5.0
2018-12-04 17:53:46 +00:00
gff2ps
biology/gff2ps: update 0.98d to 0.98l
2018-12-19 17:34:29 +00:00
gmap
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gperiodic
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graphlan
New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
2019-02-03 20:13:26 +00:00
grappa
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groopm
biology/groopm fails to build with python3
2019-01-07 09:44:42 +00:00
hisat2
New port: biology/hisat2: Program for mapping next-generation sequencing reads
2019-01-11 16:02:05 +00:00
hmmer
vec_splats function is not supported by base GCC. Add USES=compiler:c11
2019-02-18 01:30:24 +00:00
htslib
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hyphy
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
igv
biology/igv: Update 2.4.19 -> 2.5.0
2019-04-04 04:49:41 +00:00
infernal
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iolib
- Fix build in head i386
2019-04-01 19:33:15 +00:00
iqtree
biology/iqtree: Update to version 1.6.10
2019-02-21 14:33:43 +00:00
jalview
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jellyfish
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
kallisto
kallisto: Upgrade to 0.45.1, unbundle hstlib
2019-02-24 20:32:19 +00:00
lagan
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lamarc
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libgtextutils
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libsbml
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
linux-foldingathome
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mafft
…
mapm3
…
migrate
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molden
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
mopac
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +00:00
muscle
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ncbi-blast+
Update dns/libidn2 to 2.1.1
2019-02-09 23:25:36 +00:00
ncbi-cxx-toolkit
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
ncbi-toolkit
Update dns/libidn2 to 2.1.1
2019-02-09 23:25:36 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.9.4 -> 2.9.6
2019-03-31 03:31:59 +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
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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
Use real PORTVERSION of devel/p5-Parse-RecDescent
2019-04-06 14:43:14 +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
2018-12-12 01:35:33 +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
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
pbcopper
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +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
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plinkseq
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primer3
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prodigal
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
2019-02-03 18:08:14 +00:00
prodigy-lig
New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities
2019-02-03 18:49:23 +00:00
protomol
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psi88
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-biom-format
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-biopython
- Update to 1.73
2018-12-22 04:54:51 +00:00
py-bx-python
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-cutadapt
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-dnaio
biology/py-dnaio: Read and write FASTQ and FASTA
2019-03-24 19:40:26 +00:00
py-fastTSNE
biology/py-fastTSNE: Add the PORTSCOUT line
2019-03-31 16:57:54 +00:00
py-Genesis-PyAPI
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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
2018-12-12 01:35:33 +00:00
py-loompy
biology/py-loompy: Update 2.0.16 -> 2.0.17
2019-02-02 21:38:48 +00:00
py-macs2
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-orange3-bioinformatics
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +00:00
py-orange3-single-cell
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +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
2018-12-12 01:35:33 +00:00
pyfasta
- Update WWW
2019-02-07 09:30:40 +00:00
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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seaview
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seqan
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seqan1
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seqan-apps
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
seqio
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seqtk
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seqtools
biology/seqtools: fix build on current, if lld is lld7
2019-01-07 19:54:40 +00:00
sim4
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slclust
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smithwaterman
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stacks
biology/stacks: Upgrade to 2.3
2019-01-12 15:53:00 +00:00
stringtie
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t_coffee
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
tabixpp
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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
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +00:00
unanimity
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
vcflib
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vcftools
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velvet
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wise
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Makefile
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