Joseph Mingrone 32248779ba biology/diamond: Update to version 2.0.0 ... Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0		2020-07-28 02:39:00 +00:00
..
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
bedtools
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
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	Mark as BROKEN on powerpc64:	2020-05-17 02:25:16 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks	biology/cufflinks: fix build on GCC architectures	2020-07-08 10:37:07 +00:00
cytoscape
ddocent
diamond	biology/diamond: Update to version 2.0.0	2020-07-28 02:39:00 +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
grappa
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.5.15	2020-06-28 16:40:33 +00:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to version 2.0.6	2020-05-30 18:43:26 +00:00
jalview
jellyfish
kallisto
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+	Bump PORTREVISION for security/nettle shlib change	2020-05-16 10:51:32 +00:00
ncbi-cxx-toolkit
ncbi-toolkit	Bump PORTREVISION for security/nettle shlib change	2020-05-16 10:51:32 +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-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
pbbam
pbcopper	Deprecate ports broken for more than 6 months	2020-07-26 07:32:00 +00:00
pbseqan
pear-merger
phrap	Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).	2020-05-27 11:59:13 +00:00
phred
phylip
phyml	biology/phyml: update to 3.3.20200621	2020-07-10 09:45:48 +00:00
picard-tools	biology/picard-tools: CLI tools for manipulating sequencing data	2020-06-13 13:54:47 +00:00
plink
primer3
prodigal
prodigy-lig	Unbreak bulk -a	2020-06-13 15:05:44 +00:00
protomol
psi88	biology/psi88: Unbreak build with GCC 10	2020-07-04 12:15:58 +00:00
py-biom-format
py-biopython	biology/py-biopython: Set python requirement to 3.6+	2020-06-13 13:42:12 +00:00
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	biology/py-dnaio: Upgrade to 0.4.2	2020-05-24 15:23:15 +00:00
py-ete3	New port: biology/py-ete3: Framework for the analysis and visualization of trees	2020-05-16 00:13:09 +00:00
py-fastTSNE
py-Genesis-PyAPI
py-gffutils	Unbreak bulk -a	2020-07-14 07:59:28 +00:00
py-gtfparse
py-hits	New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments	2020-05-16 03:11:05 +00:00
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	Clean up some things	2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.4 -> 0.16.0	2020-06-09 05:03:48 +00:00
py-scikit-bio	biology/py-scikit-bio: Fix license	2020-05-16 02:29:20 +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
scrm	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2020-05-15 07:30:34 +00:00
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	biology/subread: Read alignment, quantification and mutation discovery	2020-06-05 01:55:49 +00:00
tabixpp
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene	biology/ugene: prepare for Qt5-5.15	2020-05-19 18:00:02 +00:00
vcflib
vcftools
velvet
viennarna
vsearch	biology/vsearch: Update to 2.15.0	2020-06-20 14:31:59 +00:00
vt	Add compiler:c++0x to USES to fix build on GCC-based systems:	2020-06-05 03:49:53 +00:00
wise
Makefile	Add rubygem-bio-shell 1.0.0	2020-07-24 07:08:11 +00:00