Joseph Mingrone c565364c26 biology/diamond: Update to version 2.0.2 ... Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.1 https://github.com/bbuchfink/diamond/releases/tag/v2.0.2		2020-08-07 11:20:11 +00:00
..
abyss
artemis
avida
babel
bamtools
bcftools	biology/bcftools: Upgrade to 1.10.2	2020-08-03 18:16:54 +00:00
bedtools
bioawk
biococoa
bolt-lmm
bowtie
bowtie2	Update devel/tbb to 2020.3 and bump dependent ports' revisions	2020-07-17 10:12:25 +00:00
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
cytoscape
ddocent
diamond	biology/diamond: Update to version 2.0.2	2020-08-07 11:20:11 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gcta
gemma
gff2ps
gmap
gperiodic
graphlan
grappa
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
hyphy
igv
infernal
iolib
iqtree
jalview
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
lamarc
libbigwig
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-toolkit
ngs-sdk
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
p5-Bio-FeatureIO
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	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
pear-merger
phrap
phred
phylip
phyml
picard-tools
plink
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt
py-dnaio
py-ete3
py-fastTSNE
py-Genesis-PyAPI
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
py-loompy
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-pyfaidx
py-pysam
py-scikit-bio
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
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
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
stringtie
subread
tabixpp	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
vcftools
velvet
viennarna
vsearch
vt	biology/vt: Patch to work with htslib 1.10.2	2020-08-03 17:42:32 +00:00
wise
Makefile	Add rubygem-bio-shell 1.0.0	2020-07-24 07:08:11 +00:00