| .. |
|
abyss
|
biology/abyss: Update 2.3.0-3 -> 2.3.1
|
2021-04-22 10:18:02 -07:00 |
|
ad2vcf
|
|
|
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
|
|
|
bbmap
|
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
|
2021-04-18 11:21:29 -05:00 |
|
bcftools
|
|
|
|
bedtools
|
|
|
|
bioawk
|
|
|
|
biococoa
|
|
|
|
biolibc
|
|
|
|
bioparser
|
|
|
|
biosoup
|
|
|
|
bolt-lmm
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
biology/bowtie2: Add support for powerpc64le
|
2021-04-18 10:53:14 -05:00 |
|
bwa
|
|
|
|
canu
|
|
|
|
cd-hit
|
|
|
|
cdbfasta
|
|
|
|
checkm
|
|
|
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
cufflinks
|
|
|
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
biology/diamond: Update to 2.0.9
|
2021-04-12 21:55:49 -03:00 |
|
dsr-pdb
|
|
|
|
edlib
|
|
|
|
emboss
|
|
|
|
exonerate
|
|
|
|
fasta
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
fasta3
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
2021-05-06 13:47:41 +02:00 |
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
|
|
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
figtree
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
|
|
|
gatk
|
|
|
|
gcta
|
|
|
|
gemma
|
|
|
|
generand
|
|
|
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
|
|
|
graphlan
|
|
|
|
groopm
|
|
|
|
haplohseq
|
|
|
|
hhsuite
|
|
|
|
hisat2
|
|
|
|
hmmer
|
|
|
|
htslib
|
|
|
|
hyphy
|
|
|
|
igv
|
|
|
|
infernal
|
|
|
|
iolib
|
|
|
|
iqtree
|
|
|
|
jalview
|
Clean up some things
|
2021-05-01 19:55:55 +02:00 |
|
jellyfish
|
|
|
|
kallisto
|
|
|
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
|
|
|
linux-foldingathome
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
2021-05-06 13:47:41 +02:00 |
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
|
|
|
molden
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
2021-05-06 13:47:41 +02:00 |
|
mopac
|
|
|
|
mothur
|
biology/mothur: Update 1.45.2 -> 1.45.3
|
2021-05-09 09:11:11 -07:00 |
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
|
|
|
ncbi-cxx-toolkit
|
|
|
|
ncbi-entrez-direct
|
biology/ncbi-entrez-direct: Update to 14.9.20210423_1
|
2021-04-26 11:53:11 -05:00 |
|
ncbi-toolkit
|
|
|
|
ncbi-vdb
|
devel/libepoll-shim: update to 0.0.20210418
|
2021-04-26 14:17:32 +00:00 |
|
ngs-sdk
|
biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH
|
2021-04-15 10:01:31 -07:00 |
|
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
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phred
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phyml
|
Clean up some things
|
2021-04-15 10:31:56 +02:00 |
|
picard-tools
|
|
|
|
plink
|
|
|
|
pooler
|
|
|
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-bigwig
|
biology/py-bigwig: Fix packaging with Python 3.8+
|
2021-04-21 09:41:29 +02:00 |
|
py-biom-format
|
|
|
|
py-biopython
|
|
|
|
py-bx-python
|
|
|
|
py-crossmap
|
biology/py-crossmap: Update to 0.5.4
|
2021-04-21 08:31:13 -05:00 |
|
py-cutadapt
|
biology/py-cutadapt: Update strict py-dnaio dep version
|
2021-05-04 08:20:39 -05:00 |
|
py-dnaio
|
biology/py-dnaio: Update to 0.5.1
|
2021-05-04 08:19:25 -05:00 |
|
py-ete3
|
|
|
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
|
|
|
py-gtfparse
|
|
|
|
py-hits
|
|
|
|
py-loompy
|
|
|
|
py-macs2
|
|
|
|
py-multiqc
|
|
|
|
py-orange3-bioinformatics
|
biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1
|
2021-04-27 01:56:19 -07:00 |
|
py-orange3-single-cell
|
|
|
|
py-pandas-charm
|
|
|
|
py-pyfaidx
|
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5
|
2021-04-23 14:57:50 -07:00 |
|
py-pysam
|
|
|
|
py-resdk
|
biology/py-resdk: Update 13.1.0 -> 13.2.0
|
2021-05-05 12:56:26 -07:00 |
|
py-scikit-bio
|
|
|
|
py-xenaPython
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
rampler
|
|
|
|
readseq
|
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
|
2021-04-18 09:20:28 -05:00 |
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
|
|
rubygem-bio-shell
|
|
|
|
samtools
|
|
|
|
scrm
|
|
|
|
seaview
|
|
|
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
|
|
|
seqio
|
|
|
|
seqkit
|
biology/seqkit: Change WWW to the project URL (from GitHub URL)
|
2021-04-16 21:00:56 -07:00 |
|
seqtk
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
biology/snpeff: Improvements to Makefile and patches
|
2021-04-19 11:41:58 -05:00 |
|
spoa
|
|
|
|
stacks
|
|
|
|
star
|
|
|
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
treekin
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ucsc-userapps
|
Deorbit RESTRICTED && NO_CDROM, part one.
|
2021-05-06 13:47:41 +02:00 |
|
ugene
|
|
|
|
vcf2hap
|
|
|
|
vcf-split
|
|
|
|
vcflib
|
|
|
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
biology/viennarna: Update 2.4.17 -> 2.4.18
|
2021-04-23 18:57:38 -07:00 |
|
vsearch
|
|
|
|
vt
|
|
|
|
wise
|
|
|
|
Makefile
|
Hook biology/ucsc-userapps to the build
|
2021-04-25 17:47:23 +00:00 |
