| .. |
|
abyss
|
|
|
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
|
|
|
bcftools
|
|
|
|
bedtools
|
|
|
|
bioawk
|
|
|
|
biococoa
|
|
|
|
bolt-lmm
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
|
|
|
bwa
|
|
|
|
canu
|
|
|
|
cd-hit
|
|
|
|
cdbfasta
|
|
|
|
checkm
|
scipy 1.5.4 is only compatible with python 3.6+
|
2020-12-24 09:03:39 +00:00 |
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
cufflinks
|
- Upgrade math/eigen3 to 3.3.8;
|
2020-12-12 17:04:37 +00:00 |
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
biology/diamond: Update to version 2.0.6
|
2020-12-20 20:21:41 +00:00 |
|
dsr-pdb
|
|
|
|
emboss
|
|
|
|
exonerate
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
|
|
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
figtree
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
|
|
|
gatk
|
|
|
|
gcta
|
- Upgrade math/eigen3 to 3.3.8;
|
2020-12-12 17:04:37 +00:00 |
|
gemma
|
- Upgrade math/eigen3 to 3.3.8;
|
2020-12-12 17:04:37 +00:00 |
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
|
|
|
graphlan
|
|
|
|
grappa
|
|
|
|
groopm
|
scipy 1.5.4 is only compatible with python 3.6+
|
2020-12-24 09:03:39 +00:00 |
|
hhsuite
|
|
|
|
hisat2
|
|
|
|
hmmer
|
|
|
|
htslib
|
|
|
|
hyphy
|
biology/hyphy: Update to version 2.5.24
|
2020-12-20 20:21:52 +00:00 |
|
igv
|
|
|
|
infernal
|
|
|
|
iolib
|
|
|
|
iqtree
|
- Upgrade math/eigen3 to 3.3.8;
|
2020-12-12 17:04:37 +00:00 |
|
jalview
|
Restrict to Java 8, since this doesn't compile with Java 11
|
2020-12-26 23:01:20 +00:00 |
|
jellyfish
|
|
|
|
kallisto
|
|
|
|
lagan
|
|
|
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
Set CMAKE options explicitly
|
2020-12-20 15:23:50 +00:00 |
|
linux-foldingathome
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
|
|
|
molden
|
|
|
|
mopac
|
|
|
|
mothur
|
|
|
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
|
|
|
ncbi-cxx-toolkit
|
|
|
|
ncbi-toolkit
|
|
|
|
ngs-sdk
|
biology/ngs-sdk: Update 2.10.5 -> 2.10.9
|
2020-12-17 20:12:12 +00:00 |
|
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
|
|
|
|
pbseqan
|
|
|
|
pear-merger
|
|
|
|
phrap
|
|
|
|
phred
|
|
|
|
phylip
|
|
|
|
phyml
|
|
|
|
picard-tools
|
|
|
|
plink
|
|
|
|
pooler
|
|
|
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-biom-format
|
|
|
|
py-biopython
|
|
|
|
py-bx-python
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-cutadapt
|
|
|
|
py-dnaio
|
|
|
|
py-ete3
|
Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to 12.8.1
|
2020-12-15 17:56:00 +00:00 |
|
py-fastTSNE
|
|
|
|
py-Genesis-PyAPI
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-gffutils
|
|
|
|
py-gtfparse
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-hits
|
|
|
|
py-loompy
|
|
|
|
py-macs2
|
|
|
|
py-multiqc
|
|
|
|
py-orange3-bioinformatics
|
|
|
|
py-orange3-single-cell
|
|
|
|
py-pandas-charm
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-pyfaidx
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-pysam
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-scikit-bio
|
|
|
|
py-xenaPython
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
pyfasta
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
python-nexus
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
rainbow
|
|
|
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
|
|
rubygem-bio-shell
|
|
|
|
samtools
|
|
|
|
scrm
|
|
|
|
seaview
|
|
|
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
|
|
|
seqio
|
|
|
|
seqtk
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
stacks
|
|
|
|
star
|
|
|
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
treekin
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ugene
|
- Update Unipro UGENE port to version 37.0
|
2020-12-31 13:43:09 +00:00 |
|
vcflib
|
|
|
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
|
|
|
vsearch
|
|
|
|
vt
|
|
|
|
wise
|
|
|
|
Makefile
|
|
|
