Jason W. Bacon c81fc00817 biology/bioawk: BWK awk modified for biological data ... Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.		2020-06-05 02:45:33 +00:00
..
abyss	biology/abyss: Update 2.2.3 -> 2.2.4	2020-05-30 09:10:44 +00:00
artemis
avida
babel
bamtools
bcftools
bedtools
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
biococoa
bolt-lmm	Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.	2020-05-06 16:11:14 +00:00
bowtie
bowtie2
bwa
canu	Mark as BROKEN on powerpc64:	2020-05-17 02:25:16 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape
ddocent
diamond	biology/diamond: Update to version 0.9.33	2020-06-03 21:44:36 +00:00
dsr-pdb
emboss	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk	biology/gatk: Update 4.1.5.0 -> 4.1.7.0	2020-05-28 02:26:51 +00:00
gcta	Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.	2020-05-06 16:11:14 +00:00
gemma	Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas	2020-05-06 16:39:12 +00:00
gff2ps
gmap
gperiodic
graphlan
grappa
groopm
haplohseq
hhsuite	biology/hhsuite: fix build on powerpc64 elfv2	2020-05-11 19:33:32 +00:00
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.5.14	2020-05-30 19:39:11 +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
linux-foldingathome	Update to 7.6.13	2020-05-09 13:21:29 +00:00
mafft
mapm3
migrate
minimap2
molden
mopac
mothur	Update devel/gmake to 4.3.	2020-05-09 19:24:49 +00:00
mrbayes	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:47:57 +00:00
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
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbcopper
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	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:51:56 +00:00
plink	Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas	2020-05-06 16:39:12 +00:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format
py-biopython	biology/py-biopython: Upgrade to 1.77	2020-05-29 02:03:29 +00:00
py-bx-python
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
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
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell	Update Sphinx	2020-05-11 23:51:58 +00:00
py-pandas-charm	Clean up some things	2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam
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	biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser	2020-05-05 14:22:09 +00:00
rubygem-bio
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
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	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
vsearch
vt	bioloty/vt: Discovers short variants from Next Generation Sequencing data	2020-06-04 18:28:13 +00:00
wise
Makefile	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00