..
abyss
Chanse update of devel/libffi
2020-07-04 18:11:42 +00:00
artemis
avida
babel
bamtools
Bump devel/jsoncpp consumers after r540853.
2020-06-30 17:46:18 +00:00
bcftools
biology/bcftools: Upgrade to 1.10.2
2020-08-03 18:16:54 +00:00
bedtools
bioawk
biococoa
bolt-lmm
bowtie
biology/bowtie: Unbreak build with GCC 10
2020-07-04 10:46:08 +00:00
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
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
2020-07-09 00:40:56 +00:00
gcta
gemma
gff2ps
gmap
gperiodic
graphlan
biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
2020-08-14 04:59:29 +00:00
grappa
groopm
biology/groopm: Remove python's 2.7 restriction placed here by mistake
2020-08-13 19:19:23 +00:00
haplohseq
hhsuite
hisat2
hmmer
htslib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
hyphy
biology/hyphy: Update to version 2.5.17
2020-08-20 16:15:22 +00:00
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
Move devel/swig30 to devel/swig and update to 4.0.1
2020-06-17 18:17:45 +00:00
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
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
2020-06-26 11:55:23 +00:00
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
biology/paml: fix the build with LLVM 11
2020-08-20 17:07:03 +00:00
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
biology/phyml: update to 3.3.20200621
2020-07-10 09:45:48 +00:00
picard-tools
plink
primer3
prodigal
prodigy-lig
protomol
psi88
biology/psi88: Unbreak build with GCC 10
2020-07-04 12:15:58 +00:00
py-biopython
py-bx-python
biology/py-bx-python: Update 0.8.8 -> 0.8.9
2020-06-26 04:17:11 +00:00
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
biology/py-loompy: Update 2.0.17 -> 3.0.6
2020-06-16 02:26:08 +00:00
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-pyfaidx
py-pysam
py-scikit-bio
devel/ipython: Update to 7.17.0
2020-08-15 12:50:57 +00:00
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
biology/seaview: Update version 5.0.3=>5.0.4
2020-06-22 17:34:44 +00:00
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
biology/vsearch: Update to 2.15.0
2020-06-20 14:31:59 +00:00
vt
biology/vt: Patch to work with htslib 1.10.2
2020-08-03 17:42:32 +00:00
wise
Makefile
Remove deprecated ports:
2020-08-15 10:50:58 +00:00
