..
abyss
artemis
Clean up after java/openjdk6 and java/openjdk6-jre removal
2019-11-26 21:46:12 +00:00
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
biococoa
bolt-lmm
bowtie
bowtie2
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
Clean up after java/openjdk6 and java/openjdk6-jre removal
2019-11-26 21:46:12 +00:00
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
fastdnaml
fastool
fastp
fastqc
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
hisat2
hmmer
htslib
hyphy
igv
infernal
iolib
iqtree
jalview
Clean up after java/openjdk6 and java/openjdk6-jre removal
2019-11-26 21:46:12 +00:00
jellyfish
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
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
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
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
biology/p5-TrimGalore: Upgrade to 0.6.5
2019-11-26 16:20:12 +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
plinkseq
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
primer3
prodigal
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
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-loompy
py-macs2
py-multiqc
biology/py-multiqc: Upgrade to 1.8
2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics
py-orange3-single-cell
py-pyfaidx
py-pysam
py-xenaPython
pycogent
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
Add USES=xorg USES=gl, ports categories b
2019-11-04 21:08:20 +00:00
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
sim4
slclust
smithwaterman
stacks
star
stringtie
t_coffee
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
tabixpp
tophat
treekin
treepuzzle
trimadap
trimmomatic
Clean up after java/openjdk6 and java/openjdk6-jre removal
2019-11-26 21:46:12 +00:00
tRNAscan-SE
ugene
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
unanimity
biology/unanimity: Remove erroneous BROKEN
2019-11-28 05:46:04 +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
