Joseph Mingrone c20d5fb7fb biology/hyphy: Update to version 2.5.10 ... Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.9 https://github.com/veg/hyphy/releases/tag/2.5.10		2020-04-25 00:33:16 +00:00
..
abyss
artemis
avida
babel
bamtools
bcftools
bedtools
biococoa
bolt-lmm
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
consed	Deprecate ports broken for more than 6 months	2020-04-04 20:51:40 +00:00
cufflinks
cytoscape
ddocent
diamond	biology/diamond: Update to version 0.9.32	2020-04-24 23:04:14 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Upgrade to 0.20.1	2020-04-09 16:17:02 +00:00
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gcta	biology/gcta: Genome-wide Complex Trait Analysis	2020-04-15 15:22:04 +00:00
gemma
gff2ps
gmap
gperiodic
graphlan
grappa
groopm
haplohseq
hhsuite	- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)	2020-04-19 09:49:02 +00:00
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.5.10	2020-04-25 00:33:16 +00:00
igv
infernal
iolib
iqtree
jalview
jellyfish
kallisto
lagan
lamarc
libbigwig
libgtextutils
libsbml
linux-foldingathome	Update to 7.6.9	2020-04-19 10:09:56 +00:00
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
mrbayes	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:47:57 +00:00
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-toolkit
ngs-sdk	biology/ngs-sdk: Update 2.10.4 -> 2.10.5	2020-04-04 20:09:00 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate	Cosmetic change	2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
p5-Bio-FeatureIO	Cosmetic change	2020-04-02 12:01:35 +00:00
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap
phred
phylip
phyml	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:51:56 +00:00
plinkseq	Deprecate ports broken for more than 6 months	2020-04-04 20:51:40 +00:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt
py-dnaio
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-loompy
py-macs2	biology/py-macs2: Upgrade to 2.2.7.1	2020-04-14 12:13:55 +00:00
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pyfaidx
py-pysam
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools	Deprecate ports broken for more than 6 months	2020-04-04 20:51:40 +00:00
sim4
slclust
smithwaterman
stacks
star	biology/star: Upgrade to 2.7.3a	2020-04-09 12:43:03 +00:00
stringtie
t_coffee	Deprecate ports broken for more than 6 months	2020-04-04 20:51:40 +00:00
tabixpp
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene	Deprecate ports broken for more than 6 months	2020-04-04 20:51:40 +00:00
vcflib
vcftools
velvet
viennarna
vsearch
wise
Makefile	biology/gcta: Genome-wide Complex Trait Analysis	2020-04-15 15:22:04 +00:00