Jason W. Bacon 5a2a6eb329 biology/peak-classifier: Classify peaks based on GFF features ... Classify ChIP/ATAC-Seq peaks based on features provided in a GFF Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources.		2021-06-14 11:40:33 -05:00
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abyss	biology/abyss: Update 2.3.0-3 -> 2.3.1	2021-04-22 10:18:02 -07:00
ad2vcf	biology/ad2vcf: Remove comment used to silence portlint	2021-06-11 10:39:02 -05:00
artemis
avida
babel
bamtools
bbmap	biology/bbmap: BBMap short read aligner, and other bioinformatic tools	2021-04-18 11:21:29 -05:00
bcftools
bedtools
bioawk
biococoa
biolibc	biology/biolibc: Remove comment used to silence portlint	2021-06-11 10:38:27 -05:00
bioparser
biosoup
bolt-lmm
bowtie
bowtie2	biology/bowtie2: Update to 2.4.4	2021-05-24 11:35:43 -05:00
bwa
canu
cd-hit	biology/cd-hit: fix build on powerpc	2021-06-10 00:35:36 +00:00
cdbfasta
checkm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
clustal-omega
clustalw
cufflinks
cytoscape	biology/cytoscape: mark unconditionally BROKEN	2021-05-12 14:55:52 +03:00
ddocent
diamond	biology/diamond: Update to 2.0.9	2021-04-12 21:55:49 -03:00
dsr-pdb
edlib
emboss
exonerate
fasta	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
fasta3	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree	biology/fasttree: fix build on powerpc	2021-06-10 12:25:31 +00:00
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gcta
gemma
generand
gff2ps
gmap
gperiodic
graphlan
groopm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to 2.5.31	2021-06-05 20:00:24 -03:00
igv
infernal
iolib	biology/iolib: Drop maintainership	2021-05-19 20:56:24 +01:00
iqtree
jalview	biology/jalview: Broken on 11	2021-06-05 11:53:07 -07:00
jellyfish
kallisto
lamarc
libbigwig
libgtextutils
libsbml	biology/libsbml: Rename LIBXML option to LIBXML2	2021-05-12 05:46:56 +08:00
linux-foldingathome	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
mafft
mapm3
migrate
minimap2	biology/minimap2: Update to 2.20	2021-05-29 16:06:34 -05:00
molden	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
mopac
mothur	biology/mothur: Update 1.45.2 -> 1.45.3	2021-05-09 09:11:11 -07:00
mrbayes	*: Remove unnecessary 'port' argument from USES=readline	2021-05-15 09:14:04 +02:00
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-entrez-direct	biology/ncbi-entrez-direct: Update to 14.9.20210423_1	2021-04-26 11:53:11 -05:00
ncbi-toolkit
ncbi-vdb	devel/libepoll-shim: update to 0.0.20210418	2021-04-26 14:17:32 +00:00
ngs-sdk	biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH	2021-04-15 10:01:31 -07:00
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
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p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
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p5-Bio-SCF
p5-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbseqan
peak-classifier	biology/peak-classifier: Classify peaks based on GFF features	2021-06-14 11:40:33 -05:00
pear-merger
phrap	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phred	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phyml	Clean up some things	2021-04-15 10:31:56 +02:00
picard-tools
plink
pooler
primer3
prodigal
prodigy-lig
protomol
psi88
py-bigwig	biology/py-bigwig: Fix packaging with Python 3.8+	2021-04-21 09:41:29 +02:00
py-biom-format
py-biopython
py-bx-python
py-crossmap	biology/py-crossmap: Update to 0.5.4	2021-04-21 08:31:13 -05:00
py-cutadapt	biology/py-cutadapt: Update strict py-dnaio dep version	2021-05-04 08:20:39 -05:00
py-dnaio	biology/py-dnaio: Update to 0.5.1	2021-05-04 08:19:25 -05:00
py-ete3
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-hits
py-loompy
py-macs2
py-multiqc	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
py-orange3-bioinformatics	biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1	2021-04-27 01:56:19 -07:00
py-orange3-single-cell
py-pandas-charm
py-pyfaidx	biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5	2021-04-23 14:57:50 -07:00
py-pysam
py-resdk	biology/py-resdk: Update 13.2.0 -> 13.3.0	2021-05-24 00:26:50 -07:00
py-scikit-bio
py-xenaPython
pyfasta
python-nexus
rainbow
rampler
readseq	biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint	2021-04-18 09:20:28 -05:00
recombine
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
samtools
scrm
seaview
seqan
seqan1
seqan3	biology/seqan3: Update 3.0.2-1195 -> 3.0.3	2021-05-29 22:38:08 -07:00
seqan-apps
seqio
seqkit	biology/seqkit: Update 0.16.0 -> 0.16.1	2021-05-19 23:02:26 -07:00
seqtk
sim4
slclust
smithwaterman
snpeff	biology/snpeff: Improvements to Makefile and patches	2021-04-19 11:41:58 -05:00
spoa
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit	2021-05-26 15:25:22 -07:00
treekin	math/lapack: +math/blas et al., upgrade to 3.9.1	2021-06-13 19:48:12 +02:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps	biology/ucsc-userapps: Update to v414	2021-05-15 10:23:08 -05:00
ugene	- Update Unipro UGENE to version 38.1 and thus unbreak	2021-05-18 15:24:55 +00:00
unikmer	biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers	2021-05-26 15:25:21 -07:00
vcf2hap	biology/vcf2hap: Remove comment used to silence portlint	2021-06-11 10:40:11 -05:00
vcf-split	biology/vcf-split: Update to 0.1.2	2021-06-11 10:05:19 -05:00
vcflib
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.17 -> 2.4.18	2021-04-23 18:57:38 -07:00
vsearch	biology/vsearch: Update to 2.17.0	2021-04-10 09:02:55 -05:00
vt
wise
Makefile	biology/peak-classifier: Classify peaks based on GFF features	2021-06-14 11:40:33 -05:00