Antoine Brodin 41a5348a3b Deprecate a few ports ... With hat: portmgr		2020-02-23 15:25:53 +00:00
..
abyss	biology/abyss: Broken on i386	2020-01-18 19:46:26 +00:00
artemis
avida
babel
bamtools	devel/jsoncpp: Update 1.8.1 -> 1.9.2	2020-01-13 21:38:35 +00:00
bcftools
bedtools
biococoa
bolt-lmm	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
bowtie
bowtie2	Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]	2019-12-26 16:25:22 +00:00
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
consed
cufflinks
cytoscape
ddocent
diamond	biology/diamond: Update to version 0.9.30	2020-02-03 15:55:05 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk	biology/gatk: Change from gradle5 to gradle6	2020-02-09 05:57:04 +00:00
gemma	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
gff2ps
gmap
gperiodic	- Update WWW	2020-01-19 09:30:22 +00:00
graphlan	Deprecate a few ports	2020-02-23 15:25:53 +00:00
grappa
groopm	Deprecate a few ports	2020-02-23 15:25:53 +00:00
haplohseq
hhsuite
hisat2
hmmer	biology/hmmer: update to 3.3	2020-01-29 05:55:12 +00:00
htslib
hyphy	biology/hyphy: Update to version 2.5.4	2020-02-21 12:22:17 +00:00
igv
infernal	biology/infernal: update to 1.1.3	2020-01-27 17:57:14 +00:00
iolib
iqtree
jalview
jellyfish
kallisto	biology/kallisto: Upgrade to 0.46.2	2020-02-15 23:09:19 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml	Clean up Makefile	2020-02-08 19:01:40 +00:00
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
mrbayes
mummer
muscle	biology/muscle: unbreak in -CURRENT	2020-01-17 16:49:03 +00:00
ncbi-blast+	biology/ncbi-blast+: Upgrade to 2.10.0	2019-12-26 16:21:17 +00:00
ncbi-cxx-toolkit
ncbi-toolkit
ngs-sdk	biology/ngs-sdk: Update 2.10.1 -> 2.10.2	2020-01-17 07:05:29 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene	Update *_DEPENDS	2020-01-08 18:36:30 +00:00
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	Update to 1.7.5	2020-01-08 18:36:35 +00:00
p5-BioPerl
p5-BioPerl-Run	Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago	2020-01-08 18:36:40 +00:00
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap
phred
phylip
phyml
plinkseq
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format	Deprecate a few ports	2020-02-23 15:25:53 +00:00
py-biopython
py-bx-python	biology/py-bx-python: Update 0.8.6 -> 0.8.8	2020-02-15 20:08:30 +00:00
py-cutadapt
py-dnaio
py-fastTSNE
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: Update 0.9 -> 0.10	2019-12-31 05:16:09 +00:00
py-gtfparse
py-loompy
py-macs2	biology/py-macs2: Bump revision for previous run dep addition	2020-02-09 14:23:43 +00:00
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.3 -> 0.15.4	2020-01-23 02:53:09 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview	biology/seaview: Update version 4.7=>5.0	2020-02-05 18:35:42 +00:00
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks
star
stringtie	biology/stringtie: fix build on GCC architectures	2020-02-23 10:52:44 +00:00
t_coffee
tabixpp
tophat
treekin	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE	biology/tRNAscan-SE: update to 2.0.5	2020-01-13 17:36:57 +00:00
ugene
vcflib
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.13 -> 2.4.14	2020-01-06 04:17:48 +00:00
vsearch	biology/vsearch: Upgrade to 2.14.2	2020-02-19 22:34:36 +00:00
wise
Makefile	Remove expired ports:	2020-01-27 15:34:18 +00:00