| .. |
|
abyss
|
devel/openmp: update to 9.0.0
|
2019-09-21 18:59:57 +00:00 |
|
artemis
|
|
|
|
avida
|
biology/avida: unbreak on powerpc64
|
2019-10-23 16:25:10 +00:00 |
|
babel
|
|
|
|
bamtools
|
|
|
|
bcftools
|
math/gsl: update to 2.6
|
2019-10-25 23:41:34 +00:00 |
|
bedtools
|
biology/bedtools: Upgrade to 2.29.0
|
2019-09-13 13:21:59 +00:00 |
|
biococoa
|
|
|
|
bolt-lmm
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
Update devel/tbb to 2019.8 and bump dependent ports' revisions
|
2019-09-25 10:03:49 +00:00 |
|
bwa
|
|
|
|
canu
|
biology/canu: Upgrade to 1.9
|
2019-11-08 14:03:15 +00:00 |
|
cd-hit
|
|
|
|
cdbfasta
|
|
|
|
checkm
|
|
|
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
consed
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
cufflinks
|
|
|
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
biology/diamond: Update to v0.9.29
|
2019-11-20 17:14:29 +00:00 |
|
dsr-pdb
|
|
|
|
emboss
|
Sprinkle more USES=xorg
|
2019-11-07 20:19:59 +00:00 |
|
exonerate
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
biology/fastahack: Upgrade to 1.0.0
|
2019-10-06 21:34:32 +00:00 |
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
|
|
|
fastqc
|
biology/fastqc: Upgrade to 0.11.8
|
2019-09-21 02:44:54 +00:00 |
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
figtree
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
gatk
|
Create devel/gradle5 in preparation of devel/gradle update
|
2019-11-20 09:51:43 +00:00 |
|
gemma
|
math/gsl: update to 2.6
|
2019-10-25 23:41:34 +00:00 |
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
a-b: Add missing USES={gnome,php,sdl,xorg}
|
2019-11-08 09:27:56 +00:00 |
|
graphlan
|
|
|
|
grappa
|
|
|
|
groopm
|
|
|
|
haplohseq
|
biology/haplohseq: Switch to distfile with example data
|
2019-11-17 15:00:13 +00:00 |
|
hhsuite
|
devel/openmp: update to 9.0.0
|
2019-09-21 18:59:57 +00:00 |
|
hisat2
|
|
|
|
hmmer
|
|
|
|
htslib
|
|
|
|
hyphy
|
|
|
|
igv
|
|
|
|
infernal
|
|
|
|
iolib
|
|
|
|
iqtree
|
|
|
|
jalview
|
|
|
|
jellyfish
|
Drop C++11 workaround for GCC < 6 after r449590
|
2019-09-14 22:01:13 +00:00 |
|
kallisto
|
biology/kallisto: Upgrade to 0.46.1
|
2019-11-06 00:18:14 +00:00 |
|
lagan
|
|
|
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
|
|
|
molden
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
mopac
|
|
|
|
mothur
|
biology/mothur: Update 1.42.3 -> 1.43.0
|
2019-10-05 17:04:42 +00:00 |
|
mrbayes
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
|
|
|
ncbi-cxx-toolkit
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
ncbi-toolkit
|
biologi/ncbi-toolkit: Remove dependency on libXp
|
2019-09-28 10:52:57 +00:00 |
|
ngs-sdk
|
|
|
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Cluster
|
|
|
|
p5-Bio-Coordinate
|
|
|
|
p5-Bio-Das
|
|
|
|
p5-Bio-Das-Lite
|
|
|
|
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-BioPerl
|
Update to 1.007006 (1.7.6)
|
2019-09-07 22:44:02 +00:00 |
|
p5-BioPerl-Run
|
|
|
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
biology/p5-TrimGalore: Upgrade to 0.6.4
|
2019-09-21 02:51:26 +00:00 |
|
paml
|
biology/paml: Update to version 4.9j
|
2019-11-22 15:32:40 +00:00 |
|
pbbam
|
biology/unanimity and dependencies: Flag as no longer open source
|
2019-11-24 15:53:00 +00:00 |
|
pbcopper
|
biology/unanimity and dependencies: Flag as no longer open source
|
2019-11-24 15:53:00 +00:00 |
|
pbseqan
|
biology/unanimity and dependencies: Flag as no longer open source
|
2019-11-24 15:53:00 +00:00 |
|
pear-merger
|
|
|
|
phrap
|
|
|
|
phred
|
|
|
|
phylip
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
phyml
|
biology/phyml: update to 3.3.20190909
|
2019-09-10 21:04:16 +00:00 |
|
plinkseq
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
primer3
|
|
|
|
prodigal
|
biology/prodigal: Eliminate a very old version from the portscout discovery process
|
2019-10-12 15:40:21 +00:00 |
|
prodigy-lig
|
|
|
|
protomol
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
psi88
|
|
|
|
py-biom-format
|
- Limit python version (does not build with 3.7+)
|
2019-11-08 12:12:42 +00:00 |
|
py-biopython
|
|
|
|
py-bx-python
|
biology/py-bx-python: Update 0.8.4 -> 0.8.6
|
2019-11-23 05:53:50 +00:00 |
|
py-cutadapt
|
biology/py-cutadapt: Upgrade to 2.7
|
2019-11-23 14:45:53 +00:00 |
|
py-dnaio
|
biology/py-dnaio: Upgrade to 0.4.1
|
2019-11-23 14:40:00 +00:00 |
|
py-fastTSNE
|
devel/openmp: update to 9.0.0
|
2019-09-21 18:59:57 +00:00 |
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
|
|
|
py-gtfparse
|
|
|
|
py-loompy
|
|
|
|
py-macs2
|
|
|
|
py-multiqc
|
biology/py-multiqc: Aggregate bioinformatics analysis reports
|
2019-09-23 16:09:30 +00:00 |
|
py-orange3-bioinformatics
|
|
|
|
py-orange3-single-cell
|
|
|
|
py-pyfaidx
|
|
|
|
py-pysam
|
|
|
|
py-xenaPython
|
|
|
|
pycogent
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
recombine
|
Fix after gets(3) retirement using gets_s(3).
|
2019-09-02 05:00:43 +00:00 |
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
samtools
|
|
|
|
seaview
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
seqan
|
|
|
|
seqan1
|
Fix some misspelled or duplicated LICENSE_*
|
2019-09-17 19:21:45 +00:00 |
|
seqan-apps
|
|
|
|
seqio
|
|
|
|
seqtk
|
|
|
|
seqtools
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
stacks
|
|
|
|
star
|
biology/star: Upgrade to 2.7.2d
|
2019-10-06 22:18:31 +00:00 |
|
stringtie
|
|
|
|
t_coffee
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
tabixpp
|
|
|
|
tophat
|
biology/tophat: Fast splice junction mapper for RNA-Seq reads
|
2019-09-27 00:49:48 +00:00 |
|
treekin
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
biology/trimmomatic: Upgrade to 0.39
|
2019-09-14 14:45:49 +00:00 |
|
tRNAscan-SE
|
|
|
|
ugene
|
Mark a few ports BROKEN, unfetchable
|
2019-11-06 12:48:32 +00:00 |
|
unanimity
|
biology/unanimity and dependencies: Flag as no longer open source
|
2019-11-24 15:53:00 +00:00 |
|
vcflib
|
|
|
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
vsearch
|
|
|
|
wise
|
a-b: Add missing USES={gnome,php,sdl,xorg}
|
2019-11-08 09:27:56 +00:00 |
|
Makefile
|
Remove expired ports:
|
2019-10-16 15:29:32 +00:00 |
b85fc34eb7